1657 COURSES Soil Microbiology 3523

Lecture Note on Soil Microbiology By Mrs. Oyeyipo, F.M.
LECTURE 1
CHARACTERISTICS OF THE SOIL ENVIRONMENT
INTRODUCTION
The soil environment consists of a variety of physical, biological and chemical factors that affect
the abundance and diversity of microbes found in the soil. At its basic level, the soil environment
consists of a solid and porous fraction. Within these fractions, a variety of chemical and physical
factors affect microbes. These include, but are not limited to texture, temperature, pH, oxygen,
cation exchange capacity and redox reactions.
The soil environment directly affects the types of microbes, as well as the rates of processes they
perform. For example, microbial activity increases with temperature, which in turn affects rates
of decomposition. On the other hand, microbial processes directly affect their environments as
well, contributing to the carbon and nitrogen cycles, which are important for microbial and plant
health. At the micro scale, bacteria and other microbes participate in a variety of reactions that
affect nutrient cycling, pH, as well as oxygen and CO 2 content. At the macro scale, these
processes can change the landscape in drastic ways, assisting in weathering of the soil and
development of soil layers.
Solid Fraction
The solid fraction of the soil consists of mineral and organic matter, which is typically about
50% of the soil by volume, and it has a dominant influence on heat, water, and chemical
transport and retention process. Most of the solid particles are derived from mineral sources such
as decomposed rocks or sediments. Soil organic matter (SOM) consists of all of the organic
components of a soil, including living biomass, decomposing tissue, and fully decomposed tissue
called humus. The rate and pathway of carbon decomposition and SOM formation directly
affects the carbon cycle. Texture can also influence chemical properties such as cation exchange
capacity (CEC). Finer textured soils with high clay content will have great CEC than soils with
low clay content.
1|Page
Figure. Volume composition of the solid and porous fractions of a typical loam surface soil.
Soil Pores
Soil pores consist of the air and water filled fractions of the soil, and together they make up
about 50% of the soil by volume. Pore space is largely determined by size and arrangement of
aggregates and affects the movement of water, air, and organisms in soil. Soil pores are typically
classified based on size: Macropores ( >75µm) Mesopores ( 30-70µm) Micropores ( 5-30µm)
Ultramicropores (0.1-5µm) Cryptoporus ( <0.1µm).
The air filled pores of the soil typically have a similar distribution of gases as the atmosphere
above the soil, with slightly lower oxygen and slightly more CO2 due to the respiration of
microorganisms. The soil atmosphere consists of about 18-20% oxygen near the surface, which
decreases with depth. CO2 is around 1%, and N2 is about 78% of the soil air filled pore space.
Oxygen content will be lower when available carbon is high (demand for high O2 to utilize
carbon). Soil that is high in clay content and/or compacted may have trouble exchanging gases to
the atmosphere. Soil air generally has a very high moisture content when compared to the
atmosphere (~100% unless the soil is very dry). The amount and composition of air in a soil is
largely determined by the water content in the soil.
The main source of soil water is rainfall and overland flow. The amount of water that enters the
soil is a function of soil structure and texture. Water moves in soil through mass flow and
capillary action. The water in soil is often called the soil solution, which can move nutrients from
the surface through the soil column. The water fraction of the pores is typically between 20% to
2|Page
30% but can vary depending on precipitation, soil texture, and soil structure. The water content
of a soil influences gas exchange, nutrient movement and concentrations of nutrients, and buffers
the temperature of the soil.
Soil Aggregates & Structure

Soil aggregates are groups of soil particles that bind to each other more strongly than to adjacent
particles. The space between the aggregates provide pore space for retention and exchange of air
and water. Aggregation affects erosion, movement of water, and plant root growth.
Polysaccharides produced by soil bacteria, and humic substances and hyphae produced by fungi
improve aggregation.
Soil structure is the arrangement of primary soil particles into aggregates which describes the
arrangement of the solid parts of the soil and the pore spaces between them. Soil structure has a
major influence on water movement, SOM leaching, and gas exchanges of the soils. The water
movement, affected by structure can bring SOM in the surface to deep inside the soil. Soil with
high clay content and/or poor structure, may have reduced infiltration and will cause runoff,
erosion and surface crusting. This can cause nutrient loss and increase the potential of
desertification.
Physical & Chemical Factors that Control Biological Activity in the Soil
Texture
Soil texture is defined as the distribution of sand (0.05-2.0 mm), silt (0.002-0.05mm), and clay
( < 0.002mm) in soil. Soil texture indirectly influences properties such as: water holding
capacity, porosity, aeration and nutrient availability. Clay particles have a very high surface to
volume ratio, which makes them very chemically active and have high nutrient availability. Due
to the adhesion of water, soils high in clay will also have a high water holding capacity. Soils
with a high clay content will often have a very active microbial community, especially in areas
of the rhizosphere.
One study by Hamarshid found that CO2 production rates were greatest in fine textured soil
compared to coarse textured soil. This was due to finer textured soils’ greater ability to hold
nutrients and water, allowing microbial populations to thrive. However, this is not always the
case, as other chemical or physical properties may affect the ability of microbes to perform
processes such as carbon decomposition. (e.g. temperature, pH and quality of substrate).
3|Page
Temperature
Soil temperature changes with depth: the surface soil (~0-20cm) is highly affected by the solar
radiation. Moving deeper (~below 27cm) temperatures are very stable over time (see figure 5).
This is because heat moves in soil mainly by conduction, which does not allow much heat to
reach deep in the soil profile. Soil temperature is also affected by the soil color, soil cover, and
the water content of the soil. A darker soil can absorb more heat compared to lighter color soil. A
dry soil is more easily heated than a wet one due to the higher heat capacity of water. Heat
moving in soil is analogous to the movement of water. Generally, the higher the temperature, the
more active microbes are, with microbial activity typically doubling with a 10° rise in
temperature. However, some bacteria thrive at very low temperatures (psychrophiles) and very
high temperatures (extremophiles).
pH
pH change in soils is due to both biotic and abiotic processes. Microbes consume and release H+
through redox reactions and fermentation. Abiotic processes such as rainfall can also affect the
pH of the soil. In areas of high rainfall, acidic soils can be created through leaching of bases from
the soil, while more basic soils are typically located in arid environments. pH affects microbial
diversity because many microbial species cannot tolerate extreme levels of pH (high or low).
Alterations in pH can render essential microbe enzymes inactive and/or denature proteins within
the cells and prevent microbial activity from occurring. However, there are microbes that can
withstand extreme pH environments. At pH below 5, fungi and acidophilic bacteria have a
competitive advantage over other bacteria that thrive at a more neutral pH.
pH can also affect the availability of nutrients in this soil. Below a pH of 5, essential plant
nutrients such as phosphorous, calcium and magnesium are not available. Low pH can also cause
aluminum (Al3+) to be released from soil minerals. Al3+ in soil solution is not only toxic to
plants and microbes, it can combine with OH- ions causing the free H+ ions to lower the pH
further.
Oxygen
Oxygen (O2) is a very important component of the productivity of both microbes and plant roots.
Oxygen has a very high electrical potential (Eh), meaning that it has a lot of potential to produce
energy when used as an electron acceptor in an oxidation-reduction reaction. An example
oxidation-reduction reaction can be seen in equation 1, where glucose is being oxidized, and
oxygen is being reduced.
4|Page
Equation 1: 6O2+C6H12O6→6CO2+6H2O
The amount of oxygen available in a soil depends on a number of factors, including soil porosity,
water content, and consumption by respiring organisms. If soil pores are large and
interconnected, oxygen can flow easily. In areas where oxygen is not present, soil microbes may
use alternative electron acceptors such as nitrate, manganese, iron, sulfate, and carbon dioxide.
An example of the result of the use of an alternative electron acceptor can be seen in figure 7.
Cation Exchange Capacity

Cation exchange capacity (CEC) is the ability of a soil to hold and exchange cations. The amount
of CEC in soil is highly dependent on the texture and organic matter of the soil. The high surface
area and negative charge of clay allows it to bind and exchange with soil solution, which
contains cations that are important for plant and microbial health.
At typical soil pH values (5-8), microbes and clay particles are both negatively charged, but
microbes still bind to clay. This binding could be due to van der waals, hydrogen bonding,
sharing electrons and ion exchange.
Redox Reactions
Reduction-oxidation (redox) reactions are chemical reactions in which reactants experience a
change in oxidation number (which means these reactants either gain or lose electrons) . Many
reactions in the soil involve the gain or loss of electrons, obtaining or releasing energy. Redox
reactions are important in the soil, because microbes obtain energy through redox reactions for
their metabolism, and the redox state can also determine the microbial processes that will occur.
Redox reactions include anabolism and catabolism process, both of which play important roles in
microbial metabolism. Anabolism is the biosynthesis of cellular components, linked to energy
requirements, while catabolism is the the biochemical processes leading to breakdown of organic
substances, linked to energy production. For example, the photosynthesis and respiration
processes are the coupled reactions in the soil, where plants required energy from light and
reduce carbon dioxide to glucose, which then be used by microbes in the soil as the energy for
their metabolism.
The tendency of compounds to accept or donate electrons is expressed as “redox potential”.

Redox potential (Eh), determined from the concentration of oxidants and reductants in the
environment, is to measure the oxidation-reduction status and electron availability within this
system. Electrons are essential to all inorganic and organic chemical reactions. Redox potential
measurements allow for rapid characterization of the degree of reduction and for predicting
5|Page
stability of various compounds that regulate nutrients and metal availability in soil and sediment.
The inorganic oxidants include oxygen, nitrate, nitrite, manganese, sulfate, and CO2, while the
reductants include various organic substrates and reduced inorganic compounds (NH4+, Fe2+,
Mn2+, S2-, CH4, and H2).
The redox potential of a substance depends on Affinity of molecules for electrons and
Concentration of reductants and oxidants (referred to as redox pair) Anaerobic environments
such as wetland soils and flooded soils are usually limited by electron acceptors and have an
abundant supply of electron donors. In this case, most microbes’ activity is limited, and
facultative and obligate microbes reduce the minerals following the electron tower. Aerated soils
are usually limited by electron donors and have an abundant supply of electron acceptors
(primarily O2).
Salinity
Soil salinity refers to the salt content in the soil. The concentrations and types of ions in solution
in the soil can cause modifications in the dispersion of the clay fraction, degrading the original
soil fraction. The sodium ion, being monovalent, increases the width of the diffuse double layer
on the surface of the clays, reducing the attractive forces between them with a consequent
increase in particle dispersion. The consequence of this dispersion of the clay is also shown by a
reduction in stability of the soil aggregates, which are thus easily transported by rain or
irrigation.
Soil salinization is a big problem for soils in arid or semi-arid regions and agricultural soils
throughout the world. Salts can adversely affect plant and microbial growth, due to destruction of
the soil structure and its consequent compacting. The stress of high salt concentration can be
detrimental for sensitive microorganisms and decrease the activity of surviving cells, due to the
metabolic load imposed by the need for stress tolerance mechanisms.
Bioavailability
Bioavailability assesses what proportion of a contaminant present at a contaminated site is
available for uptake by organisms. Bioavailability processes are the biological, chemical and
physical processes that result in an organism being exposed to a contaminant present in the soil.
These processes are: release of the contaminant from the solid phase, transport of the
contaminant to and across a biological membrane and, incorporation into a living organism.
Bioavailable molecules must cross a biological membrane, which means the molecules have to
interact with the aqueous phase. Therefore, soil properties which control partitioning between the
solid phase in soil and the pore water, such as pH, organic matter content, Eh, cation exchange
6|Page
capacity (CEC), and the concentration of clay minerals, have a significant impact on
bioavailability. Increasing exchange sites aids the retention of molecules in the pore water in a
bioavailable form, but molecules sorbed strongly to surfaces or in solid form are generally not
bioavailable.
LECTURE 2
SOIL TEXTURAL TRIANGLE
Soil Texture Triangle Activity
Using the soil texture triangle, scientists have created classes which break the distribution of
particle sizes (soil textures) into 12 categories: clay, sandy clay, silty clay, sandy clay loam, clay
loam, silty clay loam, sand, loamy sand, sandy loam, loam, silt loam, silt.
The soil texture triangle is one of the tools that soil scientists use to visualize and understand the
meaning of soil texture names. The textural triangle is a diagram which shows how each of these
12 textures is classified based on the percent of sand, silt, and clay in each.
Note that these percentages are based on the USDA definition of sand and silt only.
How to use the Soil Texture Triangle
Soil classification is typically made based on the relative proportions of silt, sand and clay.
Follow any two component percentages to find the nominal name for the soil type. For example,
30% sand, 30% clay and 40% silt:
Find 30% along the bottom (sand) line, and follow the slanted line up and to the left. Stop at the
horizontal line for 30% clay, and find the soil type: clay loam.
7|Page
Soil texture depends on its composition and the relative portions of clay, sand, and silt. In
sedimentology, clay is defined as particles of earth between 1µm and 3.9µm in diameter. (Not to
be confused with the chemical definition of clay, which is a mixture of hydrous aluminium
phyllosilicate particles and water.) Silt is defined as particles between 3.9µm and 62.5µm in
diameter, while sand is particles between 62.5µm and 2mm; in diameter.
The USDA classifies soil types according to a soil texture triangle chart which gives names to
various combinations of clay, sand, and silt. The chart can be a little confusing at first glance,
however, it makes sense after seeing a few examples.
8|Page
First, look at the orientation of the percentages on the sides of the triangle. The numbers are
arranged symmetrically around the perimeter. On the left the numbers correspond to the
percentage of clay, and on the right the numbers correspond to the percentage of silt. At the
bottom of the triangle chart are the percentages of sand.
To classify a soil sample, you find the intersection of the three lines that correspond the three
proportions. On the chart, all of the percents will add up to 100%.
Example: Classify a soil sample that is 30% clay, 15% silt, and 55% sand.First locate 30%
on the clay axis, and draw a line horizontally from left to right. Next, locate 15% on the silt axis,
and draw a line going down diagonally to the left. Finally, locate 55% on the sand axis, and draw
a line going up diagonally to the left. The intersection is in a region called Sandy Clay Loam. See
figure below. (Truthfully, you only need to make two lines.)
9|Page
Apply the same method for other samples of different compositions. As an exercise, try to
identify the following samples:
(1) 60% clay, 20% silt, 20% sand Clay

(2) 15% clay, 40% silt, 45% sand Loam
(3) 30% clay, 60% silt, 10% sand Silty Clay Loam
10 | P a g e
LECTURE 3
SOIL MICROFLORA AND FAUNA AND THEIR ACTIVITIES

Introduction
Soil biota (living things in the soil, soil organisms) consists of two broad categories – flora and
fauna. Soil organisms are a major factor in soil formation and their effects determine many
differences between soils. Soil organisms are an integral part of agricultural ecosystems. The
presence of a range of a diverse community of soil organisms is essential for the maintenance of
productive soils.
Soil organisms are responsible for a range of ecological functions and ecosystem services
including:
· nutrient cycling and nitrogen fixation,
· control of pest and diseases,
· organic matter decomposition and carbon sequestration,
· maintenance of a good soil structure for plant growth and rainwater infiltration,
· detoxification of contaminants.
Various soil organisms affect certain soil processes in different ways. An excessive reduction in
soil biodiversity, especially the loss of species with key functions, may result in severe effects
including the long-term degradation of soil and the loss of agricultural productive capacity.
Through their feeding activities, soil fauna play important roles in ecosystem dynamics as they
influence the decomposition subsystem and cycling of plant nutrients and other elements that are
of environmental importance. Soil fauna as a major group of soil biota are classified based on
their sizes, habitat, and feeding form apart from their taxonomic classification. Classification of
soil fauna based on their feeding form is also termed functional classification
Soil fauna classification based on sizes

soil fauna are classified on the basis of their sizes as microfauna, mesofauna and macrofauna.
The classification could be based on the body width or body length.
A taxonomic class of soil organisms may also be grouped based on the their sizes. For example,
members of the phylum Arthropoda are classified based on their sizes as either microathropods,
mesoarthropods or macroarthropods
11 | P a g e
Different size-groups of soil fauna may also be classified on the basis of their habitat or life
form. The habitat and life form of soil fauna are closely related to their ecosystem function.
Classification of soil fauna based on their feeding form is also termed functional classification.
The free living components of soil biota are bacteria, actinomycetes, fungi, algae as well as the
micro and macrofauna. Additionally, there is viruses which grow only within the living cells of
other organisms.
Viruses
Viruses consist of RNA and DNA molecules within protein coats. Viral particles are
metabolically inert and do not carry out respiratory or biosynthetic functions. They multiply only
within the host and induce a living host cell to produce the necessary viral components, after
assembly, the replicated viruses escape from the cell with the capability of attacking new cells.
Importance of viruses
1. Their ability to interact with host genetic material can make viruses very difficult to
control.
2. This is also the reason why they are useful as genetic transfer agents in genetic
engineering because they can serve as transfer agents a wide diversity of cells.
3. Viruses are distinguished by their ability to pass through filters capable of holding all
known bacterial types.
4. They have capability for self-reproduction and ability to cause many plant and animal
diseases. Viruses infect all categories of animals and plants from humans to microbes.
5. Viruses that infect soil organisms can persist in soil as dormant units that retain parasitic
capability.
6. The ability of viral particles pathogenic to plants and animals to survive in soil and move
into the water table is a major concern.
7. Viruses have promising prospect in biological control of weeds and obnoxious insects.
Bacteria
Bacteria are the most numerous in of the microorganisms in soil. Indeed they are the most
common of all the living organisms on the face of the earth.
12 | P a g e
They lack nuclear membranes therefore they are termed prokaryotic cells. Their cell walls are
composed principally of peptidoglycans and reproduction is by binary fission. Genetic transfer is
accomplished by conjugation and transduction.
Energy source and carbon source are useful for describing physiological differences among
bacteria and other organisms.
The majority of known bacterial species is chemoorganotrophic and is commonly referred to as
heterotrophs and a few species are chemolitotrophs.
The obligate chemolitotrophs used the same physiological pathway i.e Calvin cycle. Their
inability use any known external source of organic carbon is linked to lack of permeases to
move organic molecules across cell membranes. Therefore organic molecules must be
manufactured within the cell.
The following are some bacteria which are prominently encountered in the soil taking part in
soil processes.
Arthrobacter:
Numbers of the genus are numerically prominent in soil constituting up to 40 % of the total
plate count population. They are reported to utilize 85-180 compounds. They are slow growing
and poor competitors in the early stages of decomposition when easily decomposable materials
are rapidly attacked by other genera.
Pseudomonads:
They are aerobic except for denitrifying species that use nitrate as an alternative electron
acceptor. Most species are organotrophs, a few are facultative litothrophs using H2 or CO as an
energy source. They also occur in marine waters, some species cause plant disease, and many
nonpathogens are closely associated with plants. They attack a wide variety of organic
substrate including sugars, amino acids, alcohol and aldose sugars, hydrocarbons, oils, humic
acids and many of the synthetic pesticides.
Xanthomonas:
This is closely related to Pseudomonas, it embraces similar properties ecept that molecular
oxygen is the only electron acceptor and nitrates are not reduced. They are pathogenic to many
13 | P a g e
plants.
Sporulating Bacilli:
These members of the genus Bacillus produce heat resistant endospores and sporulation is not
repressed by exposure to air. They are mostly vigorous organotrophs and their metabolism is
strictly respiratory, strictly fermentative or both. There is great diversity within the genus as
shown by the array of products formed by different species during the course of glucose
fermentation, products include; glycerol, 2,3-butanediol, ethanol, hydrogen, acetone and
formic, acetic, lactic and succinic acids. Some species are facultative litotrophs that use H2 as an
energy source in the absence of organic carbon. Bacillus polymyxa is able to fix nitrogen.
Several species produce lytic enzymes and antibiotic that are destructive to other bacteria eg
Bacillus thuringiensis produce toxin which is pathogenic to insect lavae. Bacillus mercerans is
used for retting flax, Bacillus anthracis is a highly animal pathogen.
Clostridium:
This is a sporogenic genus, most are strict anaerobes. The genus is of economic importance
used commercially for the production of alcohols and commercial solvents. Several species such
as C butyrichum and C pasterianum fix nitrogen. They are widely distributed in soils, marine and
freshwater sediments, manures and animal intestinal tract. Some species are pathogenic to
animals, eg C tetani and C butilinum.
Azotobacter:
This is an aerobic organotrophic bacterium capable of fixing nitrogen asymbiotically. Other
genera fixing nitrogen asymbiotically are Azomonas, Beijerinkia, Dexia and Azospirillum. And
Rhizobium are known to fix nitrogen symbiotically. A related genus Agrobacterium induces
galls on hairy root but does not fix nitrogen. Nitrosomonas and Nitrobacter are
chemolithotrophic genera. Nitrosomonas convert NH4+ to NO2 - and Nitrobacter convert NO2 -
to NO3-.
Lactobacillus:
This is a fermentative organotrophic bacterium; it is commonly associated with plant herbage.
14 | P a g e
Its lactic acid production is exploited in silages, butter, milk and local dairy products.
Enterobacter is also fermentative found in animal feces and sewage; some species are widely
distributed in soil.
ACTINOMYCETES
About 90 % of the actinomycetes isolated from soil belong to the genus Streptomyces. Its
members produce a well-developed, compact branched mycelium and compact colonies on agar
plates. Reproduction is by production of aerial spores and by mycelial fragmentation. They are
intolerant of waterlogged soil, less tolerant of dessication than fungi and generally intolerant of
acidity. Thus causal organism of potato scab S scabis is controlled in poorly buffered soils such
as sand by sulphur and ammonium amendment which result in lowered soil pH. Many
Streptomyces produce antibiotics, antibacterial, antifungi, antialgal, antiviral, antiprotozoal, or
antitumor. Streptomyces also produce geosmin which is responsible for the musty smell of
freshly plowed soil and partly responsible for the musty smell of earthen cellersand old straw
piles. It appears that Streptomyces is mainly responsible for the maintenance of soil biological
balance.
FUNGI
These are the eukaryotic organisms variously referred to as mold, mildews, rusts, smuts, yeasts,
mushrooms and puffballs. Fungi are the organotrophs primarily responsible for decomposition of
organic residues even though they are always outnumbered by bacteria. Important classes
encountered in soil include;
Aerasiomycetes:
These are unicellular; the unit of structure is the uninucleate amoeba that feeds by engulfing
bacteria. Single cells characteristically aggregate into pseudoplasmodium in which the cell does
not fuse but behave as a mobile communal unit, this later change into a fruiting structure called
sporocarp which bears the asexual spores.
15 | P a g e
Myxomycetes:
These are true slime forming asexual creeping plasmodium, they are animal like in their feeding
but fungus like in their reproductive structure and spore formation. They are widely distributed
especially in association with decaying vegetation in cool moist locations.
Oomycetes:
They are found in water and soil, they are highly destructive to plant, and they produce
biflagellate asexual motile spores called zoospores. Pythium and Phythophthora are commonly
encountered in soil.
Chytridiomycetes:
They are prevalent in aquatic habitat, but also commonly encountered in soil, some members are
parasitic on algae, higher plants or insect lavae.
Zygomycetes:
They ferment different carbohydrate substrates. They are mostly saprobic, but some are
phytopathogenic, some parasite on other fungi, some produce animal trapping mechanisms. The
mucorales which are the largest order are important economically as they are used for
commercial production of alcohol and organic acids.
Ascomycetes:
Ascomycetes and Basidiomycetes are called the higher fungi. The ascomycetes are distinguished
by the formations of ascus within which are ascospores following sexual reproduction. Many of
them are saprophytic having a range of impacts e.g., plant pathogenicity, some are destructive on
materials. Others are beneficial eg the fermenting activities of yeast which has long been
exploited in beer, wine and bakeries.
Basidiomycetes:
This include a wide selection of fungi, they differ from other fungi by the production of
specialized structure called basidium. Many of them are plant parasite thus causing heavy losses
of crop and tree plants. Some are beneficial eg mycorrhizal-forming relationship with plants;
16 | P a g e
mushroom has commercial importance as edible food. They are vigorous decomposers of woody
materials.
Deuteromycetes:
This embraces fungi with septate hyphae but reproduce only by means of conidia, they do not
have a sexual reproductive phase, and they are called fungi imperfecti. They are mostly saprobic
in soil, some may be parasiticon other fungi, higher plants, humans and other animals eg species
of Aspergillus, Penicillium, Trichoderma, Fusarium.
ALGAE
Blue green algae
Cyanobacteria are the blue green algae they possess photosystem II and carry out oxygenic
photosynthesis. They contain chlorophyl A and phycobiliprotein pigments such as phycocyanin.
They exist in unicellular, colonial and filamentous forms. They have single cells, reproductive
cells or units and filamentous forms enclosed in rigid sheaths and they often show gliding
motility. They are widely distributed occurring in saline and fresh waters, in soil, on bare rocks
and sand. They also occur within the plant bodies of some liverworts, water ferns and
angiosperms. In some ecosystems cyanobacteria are of great significance because of their ability
to fix nitrogen.
Green algae
These are the eukaryotic algae they are the simplest forms of the chlorophyllus eukaryotes
distinguished from other green plants by sexual characteristics. Some green algae are unicellular
and some are multicellular. The algae are the most widely distributed of all green plants. They
are predominantly aquatic found in fresh, brackish and salt waters. Terrestrial forms occur on
rocks, mud and sand, snowfields and buildings and attached to plants and animals. Subsurface
soil samples kept moist and under illumination commonly develop algae blooms. Most algal
units found below ground are dormant forms some are however known to be facultative
organotrophs.
17 | P a g e
SOIL MICROFAUNA
These are the microfauna (less than 0.1 mm), mesofauna (0.1-10 mm) and macrofauna (greater
than 10 mm).
Microfauna
This is typified by the protozoans, they are unicellular most of which are microscopic in size but
some attain macroscopic dimensions. The group is greatly diverse in morphology and feeding
habit. All require water envelopment for metabolic activity. Five main groups are commonly
recognized; Flagellates, ciliates, naked and testate amoeba and sporozoa. Sporozoans are wholly
parasitic. Free living protozoa in soil feed on dissolved organic substances and other organism.
Many feed by grazing and predation, the soil ciliates depend primarily on bacteria for food, some
feed additionally on yeasts and other protozoa and even on small metazoan such as rotifers. The
soil an effect on the structure and functioning of microbial communities, the rise in bacteria
numbers following addition of fresh residues to soil is always followed by a rise in protozoan
numbers. Selective feesding by protozoa may alter the mix of bacterial genera. Protozoa may
accelerate nutrient cycling and their active motility in the soil water help to provide bacteria with
dissolved oxygen and nutrients.
Meso and Microfauna

These are also called metazoan, they include; the soil dwelling nematodes, millipedes,
centipedes, rotifers, mites, annelids, spiders and insects. The small members exemplified by
nematodes are able to move through existing soil pores without disturbing the soil particles. The
nematodes are also called are the most numerous of the soil metazoan, their numbers may reach
several million per square meter. The free living forms in soil are voracious feeders on both
microflora and other fauna. Earthworms constitute the major portion of the invertebrate biomass
in soil and when present are active in processing litter distributing organic matter throughout the
soil. The importance of the mesofauna in soil lies in its effect on soil and litters and on the
structure of microbial communities.
ASSOCIATION OF MICROORGANISMS WITH PLANT
18 | P a g e
Plants and microorganisms interact with each other and the interaction can be beneficial and
sometimes detrimental to either of the partners. Microorganisms are present in the different parts
of the plant and in different plants, and influence of plant on microorganism varies depending on
the part of plant and the plant. Therefore the association of microorganisms and different plant
parts are discussed below.
Association with plant roots

Plant root system occupies the soil horizon most heavily endowed with soil organic matter and
life, senescent and dead roots provide substrate materials for microbial growth. The sum total of
phenomena occurring at or near the root /soil interface has great impact both on plant welfare
and on soil organisms. The number of soil organism at successive distances from the root surface
is inversely correlated with increasing distance. For bacteria, higher population occurs within the
first 5 μm, fungal hyphae occur on the root surface and strands extend randomly for several
millimeters. The sum total of root/microbial interaction is termed
rhizosphere.
Rhizosphere
This is known generally as the soil region under the immediate influence of plant roots and in
which there is proliferation of microorganisms. The recognition that the root surface itself is a
critical site for interactions between microbes and plant led to its designation as rhizosplane.
The epidermal and cortical tissue of roots has been shown to harbor organisms other than
symbionts and pathogens. Colonized root tissue is sometimes referred to as endorhizosphere,
histophere or cortosphere. The factor primarily responsible for microbial activity in the three
zones is the available carbon contained in or emanating from plant roots. The R/S ratio i.e ratio
of organisms count in rhizosphere soil to count in root-free soil were determined for different
plant species and for single species in different soils under differing climatic regimes and at
different stages of phenology. Total microbial counts increased from 10-50 folds in the
rhizoshpere.
Root exudates
Organic materials found on, in or near roots include a wide assortment of amino, aliphatic and
aromatic acids and amides, sugars and amino sugars. In addition to soluble and diffusible
19 | P a g e
substrates is an array of insoluble materials like cellulose, lignin, protein etc. Nearly all plant
rhizosphere is expected to contain varying amounts of nearly all the simple sugars, organic acids,
and amino acids. Some of the more complex aromatic acids occur only in certain rhizospheres.
Likewise, production of certain microbial attractants and repellants is limited to certain species,
for example asparagus plant produse a diffusible glycoside that is toxic to some nematode.
Various plants are also known to produce non diffusible compounds that are biostatic or biocidal
to saprobes and root invading pathogen. Such phytoalexins include tomatin, allicin, pisatin and
phaseolin produce by tomato, onion, pea, and bean plants respectively.
Pathways for the release of plant assimilates from roots include leakage or diffusion of molecules
across cell membranes, roots secretion and extrusion and losses of cells and tissue fragments
during root growth. Root caps and tips are sites of active exudation of mucilaginous materials,
while the main root axis release mostly diffusible materials ans some mucigels. Root mucigel
consists of polysaccharides synthesized intracellularly and extruded through the cell membrane.
It is highly hydrated with fibrillar structure and contains carboxyl groups that form bondings
with clays. Mucigel is the dominant excretory product of root accounting for up to 80 % of the
total carbon loss from roots.
Association with plant shoot

Plants support abundant leaf surface organisms, this association is termed phyllosphere.
Intensity of colonization is influenced by climatic and plant factors, high humidity favours while
insolation disfavor most heterotrophs both factors favour phototrophs. Plant stems and barks are
often colonized by algae and liches. Broadleaf plants support more organisms on their leaf
surfaces than grasses. G- and yellow pigmented bacteria dominate the bacteria flora while yeasts
dominate the fungal flora.
Nonpathogenic organisms occur within the tissues of fruits, stems and leaves. The coats of seeds
prior to release from fruiting structures are sparsely colonized, during dispersal, additional
organisms either casual or contaminants or members of the phyllosphere population become seed
coat occupant.
Some seed associated organisms produce auxins, vitamins and gibberellin-like substances that
benefit emergent seedlings. Other organisms are known to produce substances that delay seed
germination and others represent plant pathogens.
20 | P a g e
Association with plant litter

The initial invaders of the aboveground litter are primarily organisms already present in the
phyllosphere. Senescent leaves before detachment suffer attack by both microflora and fauna,
standing dead wood and branches often lose half their carbon through attack mesofauna and
lignolytic fungi before becoming surface litter. As leaves and small twigs or stems fall to the
ground the numbers of bacteria there on increases sharply. The bacterial populations of moist
litter exceed that of the phyllosphere by two folds. The litter organism varies with depth and with
stage of decay. The soil fauna are more active in forest litter than in litters from grassland or
cultivated land. Fauna biomass is concentrated in the surface litter and decreases rapidly in the
underlying soil.
LECTURE 4
BIOGEOCHEMICAL CYCLE
Biogeochemical cycle or substance turnover or cycling of substances is a pathway by which

a chemical substance moves through both the biotic (biosphere) and abiotic
(lithosphere, atmosphere, and hydrosphere) components of Earth. A cycle is a series of change
which comes back to the starting point and which can be repeated. Water, for example, is always
recycled through the water cycle, as shown in the diagram. The water
undergoes evaporation, condensation, and precipitation, falling back to Earth. Elements,
chemical compounds, and other forms of matter are passed from one organism to another and
from one part of the biosphere to another through biogeochemical cycles.
The term "biogeochemical" tells us that biological, geological and chemical factors are all
involved. The circulation of chemical nutrients like carbon, oxygen, nitrogen, phosphorus,
calcium, and water etc. through the biological and physical world are known as biogeochemical
cycles. In effect, the element is recycled, although in some cycles there may be places
(called reservoirs) where the element is accumulated or held for a long period of time (such as an
ocean or lake for water).
21 | P a g e
Important cycles
The most well-known and important biogeochemical cycles, for example, include
 the carbon cycle,
 the nitrogen cycle,
 the oxygen cycle,
 the phosphorus cycle,
 the sulfur cycle,
 the water cycle,
 and the rock cycle.
The Carbon Cycle

All life is based on the element carbon. Carbon is the major chemical constituent of most
organic matter, from fossil fuels to the complex molecules (DNA and RNA) that control genetic
reproduction in organisms. Yet by weight, carbon is not one of the most abundant elements
within the Earth's crust. In fact, the lithosphere is only 0.032% carbon by weight. In comparison,
oxygen and silicon respectively make up 45.2% and 29.4% of the Earth's surface rocks.
Carbon is stored on our planet in the following major sinks: (1) as organic molecules in living
and dead organisms found in the biosphere; (2) as the gas carbon dioxide in the atmosphere;
(3) as organic matter in soils; (4) in the lithosphere as fossil fuels and sedimentary
rock deposits such as limestone, dolomite and chalk; and (5) in the oceans as dissolved
atmospheric carbon dioxide and as calcium carbonate shells in marine organisms.
22 | P a g e
Figure: The Carbon Cycle.
Ecosystems gain most of their carbon dioxide from the atmosphere. A number

of autotrophic organisms have specialized mechanisms that allow for absorption of this gas into
their cells. With the addition of water and energy from solar radiation, these organisms
use photosynthesis to chemically convert the carbon dioxide to carbon-based sugar molecules.
These molecules can then be chemically modified by these organisms through the metabolic
addition of other elements to produce more complex compounds like proteins, cellulose,
and amino acids. Some of the organic matter produced in plants is passed down
to heterotrophic animals through consumption.
Carbon dioxide enters the waters of the ocean by simple diffusion. Once dissolved in seawater,
the carbon dioxide can remain as is or can be converted into carbonate (CO 3-2) or bicarbonate
(HCO3-). Certain forms of sea life biologically fix bicarbonate with calcium (Ca +2) to
23 | P a g e
produce calcium carbonate (CaCO3). This substance is used to produce shells and other body
parts by organisms such as coral, clams, oysters, some protozoa, and some algae. When these
organisms die, their shells and body parts sink to the ocean floor where they accumulate as
carbonate-rich deposits. After long periods of time, these deposits are physically and chemically
altered into sedimentary rocks. Ocean deposits are by far the biggest sink of carbon on the
planet.
Carbon is released from ecosystems as carbon dioxide gas by the process of respiration.

Respiration takes place in both plants and animals and involves the breakdown of carbon-based
organic molecules into carbon dioxide gas and some other compound by products. The detritus
food chain contains a number of organisms whose primary ecological role is
the decomposition of organic matter into its abiotic components.
Carbon is stored in the lithosphere in both inorganic and organic forms. Inorganic deposits of

carbon in the lithosphere include fossil fuels like coal, oil, and natural gas, oil shale,
and carbonate based sedimentary deposits like limestone. Organic forms of carbon in the
lithosphere include litter, organic matter, and humic substances found in soils. Some carbon
dioxide is released from the interior of the lithosphere by volcanoes. Carbon dioxide released by
volcanoes enters the lower lithosphere when carbon-rich sediments and sedimentary rocks
are subductedand partially melted beneath tectonic boundary zones.
Since the Industrial Revolution, humans have greatly increased the quantity of carbon dioxide
found in the Earth's atmosphere and oceans. Atmospheric levels have increased by over 30%,
from about 275 parts per million (ppm) in the early 1700s to just over 365 PPM today. Scientists
estimate that future atmospheric levels of carbon dioxide could reach an amount between 450 to
600 PPM by the year 2100. The major sources of this gas due to human activities include fossil
fuel combustion and the modification of natural plant cover found in grassland, woodland, and
forested ecosystems. Emissions from fossil fuel combustion account for about 65% of the
additional carbon dioxide currently found in the Earth's atmosphere. The other 35% is derived
from deforestation and the conversion of natural ecosystems into agricultural systems.
Researchers have shown that natural ecosystems can store between 20 to 100 times more carbon
24 | P a g e
dioxide than agricultural land-use types.
The Nitrogen Cycle
The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into various

chemical forms as it circulates among the atmosphere and terrestrial and marine ecosystems. The
conversion of nitrogen can be carried out through both biological and physical processes.
Important processes in the nitrogen cycle include fixation, ammonification, nitrification,
and denitrification. The majority of Earth's atmosphere (78%) is nitrogen, making it the largest
pool of nitrogen. However, atmospheric nitrogen has limited availability for biological use,
leading to a scarcity of usable nitrogen in many types of ecosystems. The nitrogen cycle is of
particular interest to ecologists because nitrogen availability can affect the rate of key ecosystem
processes, including primary production and decomposition. Human activities such as fossil fuel
combustion, use of artificial nitrogen fertilizers, and release of nitrogen in wastewater have
dramatically altered the global nitrogen cycle.
25 | P a g e
Figure: Nitrogen cycle
The processes of the nitrogen cycle
o 1 Nitrogen fixation
o 2 Assimilation
o 3 Ammonification
o 4 Nitrification
o 5 Denitrification
o 6 Anaerobic ammonia oxidation
o 7 Other processes
Nitrogen is present in the environment in a wide variety of chemical forms including organic
nitrogen, ammonium (NH+4), nitrite (NO−2), nitrate (NO−3), nitrous oxide (N2O), nitric
oxide (NO) or inorganic nitrogen gas (N2). Organic nitrogen may be in the form of a living
organism, humus or in the intermediate products of organic matter decomposition. The processes
of the nitrogen cycle transform nitrogen from one form to another. Many of those processes are
carried out by microbes, either in their effort to harvest energy or to accumulate nitrogen in a
26 | P a g e
form needed for their growth. For example, the nitrogenous wastes in animal urine are broken
down by nitrifying bacteria in the soil to be used anew. The diagram above shows how these
processes fit together to form the nitrogen cycle.
Nitrogen fixation
Atmospheric nitrogen must be processed, or "fixed", in a usable form to be taken up by plants.

Between 5x1012 and 10x1012 g per year are fixed by lightning strikes, but most fixation is done
by free-living or symbiotic bacteria known as diazotrophs. These bacteria have
the nitrogenase enzyme that combines gaseous nitrogen with hydrogen to produce ammonia,
which is converted by the bacteria into other organic compounds. Most biological nitrogen
fixation occurs by the activity of Mo-nitrogenase, found in a wide variety of bacteria and
some Archaea. Mo-nitrogenase is a complex two-component enzyme that has multiple metal-
containing prosthetic groups. An example of the free-living bacteria is Azotobacter. Symbiotic
nitrogen-fixing bacteria such as Rhizobium usually live in the root nodules of legumes (such as
peas, alfalfa, and locust trees). Here they form a mutualistic relationship with the plant,
producing ammonia in exchange for carbohydrates. Because of this relationship, legumes will
often increase the nitrogen content of nitrogen-poor soils. A few non-legumes can also form
such symbioses. Today, about 30% of the total fixed nitrogen is produced industrially using
the Haber-Bosch process, which uses high temperatures and pressures to convert nitrogen gas
and a hydrogen source (natural gas or petroleum) into ammonia.
Assimilation
Plants take nitrogen from the soil by absorption through their roots as amino acids,
nitrate ions, nitrite ions, or ammonium ions. Most nitrogen obtained by terrestrial animals can be
traced back to the eating of plants at some stage of the food chain.
Plants can absorb nitrate or ammonium from the soil via their root hairs. If nitrate is absorbed, it
is first reduced to nitrite ions and then ammonium ions for incorporation into amino acids,
nucleic acids, and chlorophyll.In plants that have a symbiotic relationship with rhizobia, some
nitrogen is assimilated in the form of ammonium ions directly from the nodules. It is now known
that there is a more complex cycling of amino acids between Rhizobia bacteroids and plants. The
plant provides amino acids to the bacteroids so ammonia assimilation is not required and the
27 | P a g e
bacteroids pass amino acids (with the newly fixed nitrogen) back to the plant, thus forming an
interdependent relationship.While many animals, fungi, and other heterotrophic organisms obtain
nitrogen by ingestion of amino acids, nucleotides, and other small organic molecules, other
heterotrophs (including many bacteria) are able to utilize inorganic compounds, such as
ammonium as sole N sources. Utilization of various N sources is carefully regulated in all
organisms.
Ammonification
When a plant or animal dies or an animal expels waste, the initial form of nitrogen is organic.
Bacteria or fungi convert the organic nitrogen within the remains back into ammonium (NH+
4), a process called ammonification or mineralization. Enzymes involved are:
 GS: Gln Synthetase (Cytosolic & Plastic)

 GOGAT: Glu 2-oxoglutarate aminotransferase (Ferredoxin &
NADH-dependent)
 GDH: Glu Dehydrogenase:
 Minor Role in ammonium assimilation.
 Important in amino acid catabolism.
Nitrification
The conversion of ammonium to nitrate is performed primarily by soil-living bacteria and other
nitrifying bacteria. In the primary stage of nitrification, the oxidation of ammonium (NH+
4) is performed by bacteria such as the Nitrosomonas species, which converts ammonia
to nitrites (NO−2). Other bacterial species such as Nitrobacter, are responsible for the oxidation
of the nitrites (NO−2) into nitrates (NO−3). It is important for the ammonia (NH3) to be converted
to nitrates or nitrites because ammonia gas is toxic to plants.
Due to their very high solubility and because soils are highly unable to retain anions, nitrates can
enter groundwater. Elevated nitrate in groundwater is a concern for drinking water use because
nitrate can interfere with blood-oxygen levels in infants and cause methemoglobinemia or blue-
baby syndrome. Where groundwater recharges stream flow, nitrate-enriched groundwater can
contribute to eutrophication, a process that leads to high algal population and growth, especially
28 | P a g e
blue-green algal populations. While not directly toxic to fish life, like ammonia, nitrate can have
indirect effects on fish if it contributes to this eutrophication. Nitrogen has contributed to severe
eutrophication problems in some water bodies. Since 2006, the application of
nitrogen fertilizer has been increasingly controlled in Britain and the United States. This is
occurring along the same lines as control of phosphorus fertilizer, restriction of which is
normally considered essential to the recovery of eutrophied waterbodies.
Denitrification
Denitrification is the reduction of nitrates back into nitrogen gas (N 2), completing the nitrogen
cycle. This process is performed by bacterial species such as Pseudomonas and Clostridium in
anaerobic conditions.They use the nitrate as an electron acceptor in the place of oxygen during
respiration. These facultatively anaerobic bacteria can also live in aerobic conditions.
Denitrification happens in anaerobic conditions e.g. waterlogged soils. The denitrifying bacteria
use nitrates in the soil to carry out respiration and consequently produce nitrogen gas, which is
inert and unavailable to plants.
Anaerobic ammonia oxidation
In this biological process, nitrite and ammonia are converted directly into

molecular nitrogen (N2) gas. This process makes up a major proportion of nitrogen conversion in
the oceans.
Other processes
Though nitrogen fixation is the primary source of plant-available nitrogen in most ecosystems, in
areas with nitrogen-rich bedrock, the breakdown of this rock also serves as a nitrogen source
Water Cycle
The water cycle is the cycle that water goes through on Earth. Water is essential for life as we
know it. It is present throughout the Solar System, and was part of the Earth from its formation.
The source of the water was the same as the source of the Earth's rock: the cloud of particles
which condensed in the origin of the solar system.
29 | P a g e
Figure: The water cycle
The cycle
 First, water on the surface of the Earth evaporates.

 Then, water collects as water vapor in the sky. This
makes clouds.
 Next, the water in the clouds gets cold. This makes it
become liquid again. This process is called condensation.
 Then, the water falls from the sky as rain, snow, sleet or hail.
This is called precipitation.
 The water sinks into the surface and also collects
into lakes, oceans, or aquifers. It evaporates again and continues
the cycle.
Phosphorus Cycle
30 | P a g e
Phosphorus Cycle on land
The phosphorus cycle is the biogeochemical cycle that describes the movement

of phosphorus through the lithosphere, hydrosphere, and biosphere. Unlike many other
biogeochemical cycles, the atmosphere does not play a significant role in the movement of
phosphorus, because phosphorus and phosphorus-based compounds are usually solids at the
typical ranges of temperature and pressure found on Earth. The production of phosphine gas
occurs in only specialized, local conditions.
On the land, phosphorus (chemical symbol, P) gradually becomes less available to plants over
thousands of years, because it is slowly lost in runoff. Low concentration of P in soils reduces
plant growth, and slows soil microbial growth - as shown in studies of soil microbialbiomass.
Soil microorganisms act as both sinks and sources of available P in the biogeochemical
cycle. Locally, transformations of P are chemical, biological and microbiological: the major
long-term transfers in the global cycle, however, are driven by tectonic movements in geologic
time.
Humans have caused major changes to the global P cycle through shipping of P minerals, and
31 | P a g e
use of P fertilizer, and also the shipping of food from farms to cities, where it is lost as effluent
The aquatic phosphorus cycle
Ecological function
Phosphorus is an essential nutrient for plants and animals. Phosphorus is a limiting nutrient for
aquatic organisms. Phosphorus forms parts of important life-sustaining molecules that are very
common in the biosphere. Phosphorus does not enter the atmosphere, remaining mostly on land
and in rock and soil minerals. Eighty percent of the mined phosphorus is used to make fertilizers.
Phosphates from fertilizers, sewage and detergents can cause pollution in lakes and streams.
Overenrichment of phosphate in both fresh and inshore marine waters can lead to massive algae
blooms which, when they die and decay, leads to eutrophication of fresh waters only. An
example of this is the Canadian Experimental Lakes Area. These freshwater algal blooms should
not be confused with those in saltwater environments. Recent research suggests that the
predominant pollutant responsible for algal blooms in salt water estuaries and coastal marine
habitats is Nitrogen.
32 | P a g e
Phosphorus occurs most abundantly in nature as part of the orthophosphate ion (PO4)3−,

consisting of a P atom and 4 oxygen atoms. On land most phosphorus is found in rocks and
minerals. Phosphorus rich deposits have generally formed in the ocean or from guano, and over
time, geologic processes bring ocean sediments to land. Weathering of rocks and minerals
release phosphorus in a soluble form where it is taken up by plants, and it is transformed into
organic compounds. The plants may then be consumed by herbivores and the phosphorus is
either incorporated into their tissues or excreted. After death, the animal or plant decays, and
phosphorus is returned to the soil where a large part of the phosphorus is transformed into
insoluble compounds. Runoff may carry a small part of the phosphorus back to the ocean.
Generally with time (thousands of years) soils become deficient in phosphorus leading to
ecosystem retrogression.
Biological function
The primary biological importance of phosphates is as a component of nucleotides, which serve

as energy storage within cells (ATP) or when linked together, form the nucleic
acids DNA and RNA. The double helix of our DNA is only possible because of the phosphate
ester bridge that binds the helix. Besides making biomolecules, phosphorus is also found in bone
and the enamel of mammalian teeth, whose strength is derived from calcium phosphate in the
form of Hydroxylapatite. It is also found in the exoskeleton of insects, and phospholipids (found
in all biological membranes). It also functions as a buffering agent in maintaining acid
base homeostasis in the human body.
Process of the cycle
Phosphates move quickly through plants and animals; however, the processes that move them
through the soil or ocean are very slow, making the phosphorus cycle overall one of the slowest
biogeochemical cycles.
Initially, phosphate weathers from rocks and minerals, the most common mineral being apatite.
Overall small losses occur in terrestrial environments by leaching and erosion, through the action
of rain. In soil, phosphate is adsorbed on iron oxides, aluminium hydroxides, clay surfaces, and
organic matter particles, and becomes incorporated (immobilized or fixed). Plants and fungi can
also be active in making P soluble.
33 | P a g e
Unlike other cycles, P is not normally found in the air as a gas; it only occurs under highly
reducing conditions as the gas phosphine PH3
Mineral Transformation by Microorganisms
Microorganisms are intimately involved in mineral/metal biogeochemistry with a variety of

processes determining mobility, and bioavailability. The balance between mobilization and
immobilization varies depending on the organisms involved, their environment and physico-
chemical conditions. Mineral/Metal mobilization can arise from leaching mechanisms,
complexation by metabolites and siderophores, and methylation where this results in
volatilization. Immobilization can result from sorption, transport and intracellular sequestration
or precipitation as organic and inorganic compounds, e.g. oxalates (fungi) and sulfides. In
addition, reduction of higher-valency species may effect mobilization, e.g Mn(IV) to Mn(II), or
immobilization, e.g. Cr(VI) to Cr(III).
In terrestrial environments, fungi serve as neglected but important geochemical agents. Fungi
promote rock weathering and contribute to the dissolution of mineral aggregates in soil through
excretion of H+, organic acids and other ligands, or through redox transformations of mineral
constituents. The main mechanism of metal mobilization from insoluble metal minerals is a
combination of acidification and ligand-promoted dissolution: if oxalic acid is produced the
production of metal oxalates can occur. Fungi can therefore also play an active or passive role in
mineral formation through precipitation of secondary minerals, e.g. oxalates, and through the
nucleation of crystalline material onto cell walls that can result in the formation of biogenic
micro-fabrics within mineral substrates. Such interactions between fungi and minerals are of
importance to biogeochemical cycles including those of C, N, S and P. It has been shown that
fungi may play an important role in the transformation of micro-fabrics in limestone (CaCO3)
and dolomite (CaMg(CO3)2) and have produced direct evidence of mineralized fungal filaments
with secondary carbonates. Other experiments using laboratory microcosms showed that fungi
can precipitate calcite (CaCO3) and whewellite (calcium oxalate monohydrate, CaC2O4.H2O).
Other processes that can determine metal bioavailability are important microbially-catalyzed
reactions of the natural sulfur cycle. Chemolithotrophic leaching by sulfur/sulfide-oxidizing
bacteria can result in mobilization from polluted soil matrices, while sulfide production by SRB
can result in precipitation of soluble metals as insoluble sulfides, with other redox
34 | P a g e
transformations also being mediated by these organisms, e.g. Cr(VI) to Cr(III). Findings have
also shown that metals such as Cd, Co, Cr, Cu, Mn, Ni and Zn can be efficiently leached from
contaminated soils, and removed from solution by SRB. In addition, SRB can reduce metalloid
oxyanions such as selenite to elemental selenium.also, SRB, growing as a biofilm, can mediate
formation of elemental sulfur in the presence of selenite. The indirect, enzymatically-mediated
coprecipitation of sulfur and selenium is a generalised ability among SRB, arising from sulfide
biogenesis, and can take place under low redox conditions and in the dark.
LECTURE 5
BIODEGRADATION AND BIOGENERATION
Biodegradation is the disintegration of materials by bacteria, fungi, or other biological means.

Although often conflated, biodegradable is distinct in meaning from compostable. While
biodegradable simply means to be consumed by microorganisms, "compostable" makes the
specific demand that the object break down under composting conditions. The term is often used
in relation to ecology, waste management, biomedicine, and the natural environment
(bioremediation) and is now commonly associated with environmentally friendly products that
are capable of decomposing back into natural elements. Organic material can be
degraded aerobically with oxygen, or anaerobically, without oxygen. Biosurfactant, an
extracellular surfactant secreted by microorganisms, enhances the biodegradation process.
Biodegradable matter is generally organic material that serves as a nutrient for microorganisms.

Microorganisms are so numerous and diverse that, a huge range of compounds are biodegraded,
including hydrocarbons (e.g.oil), polychlorinatedbiphenyls (PCBs), polyaromatic
hydrocarbons (PAHs), plant materials, pharmaceutical substances. Decomposition of
biodegradable substances may include both biological and abiotic steps.
For example, sewage flows to the wastewater treatment plant where many of the organic
compounds are broken down; some compounds are simply biotransformed (changed), others are
completely mineralized . These biodegradation processes are essential to recycle wastes so that
the elements in them can be used again, a term also referred to as “biogeneration”. Recalcitrant
materials, which are hard to break down, may enter the environment as contaminants.
Biodegradation is a microbial process that occurs when all of the nutrients and physical
conditions involved are suitable for growth. Temperature is an important variable; keeping a
35 | P a g e
substance frozen can prevent biodegradation. Most biodegradation occurs at temperatures

between 10 and 35°C. Water is essential for biodegradation. To prevent the biodegradation of
cereal grains in storage, they must be kept dry. Foods such as bread or fruit will support the
growth of mold if the moisture level is high enough. The microorganisms need energy plus
carbon, nitrogen, oxygen, phosphorus, sulfur, calcium, magnesium, and several metals to grow
and reproduce. The oxidation of organic substances to carbon dioxide and water is
an exothermic (heat-releasing) process. For each mole of oxygen used as electron acceptor
(oxidant), about 104 kilocalories (435 kJ) of energy is potentially available. All organisms make
use of only part of this energy. The rest is lost as heat. This can be seen in composting when the
compost becomes hot. Biodegradation can occur under aerobic conditions where oxygen is the
electron acceptor and under anaerobic conditions where nitrate, sulfate, or another compound is
the electron acceptor.
Bioremediation
Bioremediation is defined as the use of biological processes to degrade, break down, transform,
and/or essentially remove contaminants or impairments of quality from soil and water.
Bioremediation is a natural process which relies on bacteria, fungi, and plants to alter
contaminants as these organisms carry out their normal life functions. Metabolic processes of
these organisms are capable of using chemical contaminants as an energy source, rendering the
contaminants harmless or less toxic products in most cases.
Many substances known to have toxic properties have been introduced into the environment
through human activity. These substances range in degree of toxicity and danger to human
health. Many of these substances either immediately or ultimately come in contact with and are
sequestered by soil. Conventional methods to remove, reduce, or mitigate toxic substances
introduced into soil or ground water via anthropogenic activities and processes include pump and
treat systems, soil vapor extraction, incineration, and containment. Utility of each of these
conventional methods of treatment of contaminated soil and/or water suffers from recognizable
drawbacks and may involve some level of risk.
The emerging science and technology of bioremediation offers an alternative method to detoxify
contaminants. Bioremediation has been demonstrated and is being used as an effective means of
mitigating:
 hydrocarbons
36 | P a g e
 halogenated organic solvents

 halogenated organic compounds
 non-chlorinated pesticides and herbicides
 nitrogen compounds
 metals (lead, mercury, chromium)
 radionuclides
Bioremediation technology exploits various naturally occurring mitigation processes: natural

attenuation, biostimulation, and bioaugmentation. Bioremediation which occurs without
human intervention other than monitoring is often called natural attenuation. This natural
attenuation relies on natural conditions and behavior of soil microorganisms that are indigenous
to soil. Biostimulation also utilizes indigenous microbial populations to remediate contaminated
soils. Biostimulation consists of adding nutrients and other substances to soil to catalyze natural
attenuation processes. Bioaugmentation involves introduction of exogenic microorganisms
(sourced from outside the soil environment) capable of detoxifying a particular contaminant,
sometimes employing genetically altered microorganisms.
During bioremediation, microbes utilize chemical contaminants in the soil as an energy source
and, through oxidation-reduction reactions, metabolize the target contaminant into useable
energy for microbes. By-products (metabolites) released back into the environment are typically
in a less toxic form than the parent contaminants. For example, petroleum hydrocarbons can be
degraded by microorganisms in the presence of oxygen through aerobic respiration. The
hydrocarbon loses electrons and is oxidized while oxygen gains electrons and is reduced. The
result is formation of carbon dioxide and water. When oxygen is limited in supply or absent, as
in saturated or anaerobic soils or lake sediment, anaerobic (without oxygen) respiration prevails.
Generally, inorganic compounds such as nitrate, sulfate, ferric iron, manganese, or carbon
dioxide serve as terminal electron acceptors to facilitate biodegradation.
Three primary ingredients for bioremediation are: 1) presence of a contaminant, 2) an electron

acceptor, and 3) presence of microorganisms that are capable of degrading the specific
contaminant. Generally, a contaminant is more easily and quickly degraded if it is a naturally
occurring compound in the environment, or chemically similar to a naturally occurring
compound, because microorganisms capable of its biodegradation are more likely to have
37 | P a g e
evolved. Petroleum hydrocarbons are naturally occurring chemicals; therefore, microorganisms

which are capable of attenuating or degrading hydrocarbons exist in the soil environment.
Development of biodegradation technologies of synthetic chemicals such DDT is dependent on
outcomes of research that searches for natural or genetically improved strains of microorganisms
to degrade such contaminants into less toxic forms.
Microorganisms have limits of tolerance for particular environmental conditions, as well as

optimal conditions for pinnacle performance. Factors that affect success and rate of microbial
biodegradation are nutrient availability, moisture content, pH, and temperature of the soil matrix.
Inorganic nutrients including, but not limited to, nitrogen, and phosphorus are necessary for
microbial activity and cell growth. It has been shown that “treating petroleum-contaminated soil
with nitrogen can increase cell growth rate, decrease the microbial lag phase, help to maintain
microbial populations at high activity levels, and increase the rate of hydrocarbon degradation”.
However, it has also been shown that excessive amounts of nitrogen in soil cause microbial
inhibition.
All soil microorganisms require moisture for cell growth and function. Availability of water
affects diffusion of water and soluble nutrients into and out of microorganism cells. However,
excess moisture, such as in saturated soil, is undesirable because it reduces the amount of
available oxygen for aerobic respiration. Anaerobic respiration, which produces less energy for
microorganisms (than aerobic respiration) and slows the rate of biodegradation, becomes the
predominant process. Soil moisture content “between 45 and 85 percent of the water-holding
capacity (field capacity) of the soil or about 12 percent to 30 percent by weight” is optimal for
petroleum hydrocarbon degradation.
Soil pH is important because most microbial species can survive only within a certain pH range.
Furthermore, soil pH can affect availability of nutrients. Biodegradation of petroleum
hydrocarbons is optimal at a pH 7 (neutral); the acceptable range is pH 6 – 8.
Temperature influences rate of biodegradation by controlling rate of enzymatic reactions within

microorganisms. Generally, “speed of enzymatic reactions in the cell approximately doubles for
each 10oC rise in temperature”. There is an upper limit to the temperature that microorganisms
can withstand. Most bacteria found in soil, including many bacteria that degrade petroleum
hydrocarbons, are mesophiles which have an optimum temperature ranging from 25 degree C to
38 | P a g e
45 degree C. Thermophilic bacteria (those which survive and thrive at relatively high
temperatures) which are normally found in hot springs and compost heaps exist indigenously in
cool soil environments and can be activated to degrade hydrocarbons with an increase in
temperature to 60 degree C. This finding “suggested an intrinsic potential for natural attenuation
in cool soils through thermally enhanced bioremediation techniques”.
Contaminants can adsorb to soil particles, rendering some contaminants unavailable to

microorganisms for biodegradation. Thus, in some circumstances, bioavailability of
contaminants depends not only on the nature of the contaminant but also on soil type.
Hydrophobic contaminants, like petroleum hydrocarbons, have low solubility in water and tend
to adsorb strongly in soil with high organic matter content. In such cases, surfactants are utilized
as part of the bioremediation process to increase solubility and mobility of these contaminants.
Additional research findings of the existence of thermophilic bacteria in cool soil also suggest
that high temperatures enhance the rate of biodegradation by increasing the bioavailability of
contaminants. It is suggested that contaminants adsorbed to soil particles are mobilized and their
solubility increased by high temperatures.
Soil type is an important consideration when determining the best suited bioremediation
approach to a particular situation. In situ bioremediation refers to treatment of soil in place. In
situ biostimulation treatments usually involve bioventing, in which oxygen and/or nutrients are
pumped through injection wells into the soil. It is imperative that oxygen and nutrients are
distributed evenly throughout the contaminated soil. Soil texture directly affects the utility of
bioventing, in as much as permeability of soil to air and water is a function of soil texture. Fine-
textured soils like clays have low permeability, which prevents biovented oxygen and nutrients
from dispersing throughout the soil. It is also difficult to control moisture content in fine textured
soils because their smaller pores and high surface area allow it to retain water. Fine textured soils
are slow to drain from water-saturated soil conditions, thus preventing oxygen from reaching soil
microbes throughout the contaminated area. Bioventing is well-suited for well-drained, medium,
and coarse-textured soils.
In situ bioremediation causes minimal disturbance to the environment at the contamination site.

In addition, it incurs less cost than conventional soil remediation or removal and replacement
treatments because there is no transport of contaminated materials for off-site treatment.
39 | P a g e
However, in situ bioremediation has some limitations: 1) it is not suitable for all soils, 2)
complete degradation is difficult to achieve, and 3) natural conditions (i.e. temperature) are hard
to control for optimal biodegradation. Ex situ bioremediation, in which contaminated soil is
excavated and treated elsewhere, is an alternative.
LECTURE 6
EFFECT OF PESTICIDES AND OTHER CHEMICALS IN THE ENVIRONMENT

Pesticides are substances meant for attracting, seducing, and then destroying any pest. They are
a class of biocide. The most common use of pesticides is as plant protection products (also
known as crop protection products), which in general protect plants from damaging influences
such as weeds, fungi, or insects. This use of pesticides is so common that the term pesticide is
often treated as synonymous with plant protection product, although it is in fact a broader term,
as pesticides are also used for non-agricultural purposes.
The term pesticide includes all of the following: herbicide, insecticide, insect growth

regulator, nematicide,termiticide, molluscicide, piscicide, avicide, rodenticide,
predacide, bactericide, insectrepellent, animalrepellent, antimicrobial, fungicide, disinfectant (ant
imicrobial), and sanitizer.
In general, a pesticide is a chemical or biological agent (such as

a virus, bacterium, antimicrobial, or disinfectant) that deters, incapacitates, kills, or otherwise
discourages pests. Target pests can include insects, plant pathogens,
weeds, mollusks, birds, mammals, fish, nematodes (roundworms), and microbes that destroy
property, cause nuisance, or spread disease, or are disease vectors. Although pesticides have
benefits, some also have drawbacks, such as potential toxicity to humans and other species.
According to the Stockholm Convention on Persistent Organic Pollutants, 9 of the 12 most
dangerous and persistent organic chemicals are organochlorine pesticides.
Types of Pesticides
Pesticides are often referred to according to the type of pest they control. Pesticides can also be
considered as either biodegradable pesticides, which will be broken down by microbes and other
40 | P a g e
living beings into harmless compounds, or persistent pesticides, which may take months or years
before they are broken down: it was the persistence of DDT, for example, which led to its
accumulation in the food chain and its killing of birds of prey at the top of the food chain.
Another way to think about pesticides is to consider those that are chemical pesticides or are
derived from a common source or production method.
Some examples of chemically-related pesticides are:
Organophosphate pesticides
Organophosphates affect the nervous system by disrupting, acetylcholinesterase activity, the

enzyme that regulates acetylcholine, a neurotransmitter. Most organophosphates are insecticides.
They were developed during the early 19th century, but their effects on insects, which are similar
to their effects on humans, were discovered in 1932. Some are very poisonous. However, they
usually are not persistent in the environment.
Carbamate pesticides
Carbamate pesticides affect the nervous system by disrupting an enzyme that regulates
acetylcholine, a neurotransmitter. The enzyme effects are usually reversible. There are several
subgroups within the carbamates
Organochlorine insecticides
They were commonly used in the past, but many have been removed from the market due to their
health and environmental effects and their persistence (e.g., DDT, chlordane, and toxaphene).
Pyrethroid pesticides
They were developed as a synthetic version of the naturally occurring pesticide pyrethrin, which
is found in chrysanthemums. They have been modified to increase their stability in the
environment. Some synthetic pyrethroids are toxic to the nervous system.
Sulfonylurea herbicides
The following sulfonylureas have been commercialized for weed control: amidosulfuron,
azimsulfuron, bensulfuron-methyl, chlorimuron-ethyl, ethoxysulfuron, flazasulfuron,
flupyrsulfuron-methyl-sodium, halosulfuron-methyl, imazosulfuron, nicosulfuron, oxasulfuron,
primisulfuron-methyl, pyrazosulfuron-ethyl, rimsulfuron, sulfometuron-methyl Sulfosulfuron,
41 | P a g e
terbacil, bispyribac-sodium, cyclosulfamuron, and pyrithiobac-

sodium. Nicosulfuron, triflusulfuron methyl and chlorsulfuron are broad-spectrum herbicides
that kill plants by inhibiting the enzyme acetolactate synthase. In the 1960s, more than 1 kg/ha
(0.89 lb/acre) crop protection chemical was typically applied, while sulfonylureates allow as
little as 1% as much material to achieve the same effect.
Biopesticides
Biopesticides are certain types of pesticides derived from such natural materials as animals,
plants, bacteria, and certain minerals. For example, canola oil and baking soda have pesticidal
applications and are considered biopesticides. Biopesticides fall into three major classes:
Microbial pesticides which consist of bacteria, entomopathogenic fungi or viruses (and

sometimes includes the metabolites that bacteria or fungi produce).
Entomopathogenic nematodes are also often classed as microbial pesticides, even though they
are multi-cellular.
Biochemical pesticides or herbal pesticides are naturally occurring substances that control (or
monitor in the case of pheromones) pests and microbial diseases.
Plant-incorporated protectants (PIPs) have genetic material from other species incorporated into
their genetic material (i.e. GM crops). Their use is controversial, especially in many European
countries.
Classification based on type of pest
Pesticides that are related to the type of pests are:
Type Action
Control algae in lakes, canals, swimming pools, water tanks, and

Algicides
other sites
42 | P a g e
Kill or repel organisms that attach to underwater surfaces, such as

Antifouling agents
boat bottoms
Antimicrobials Kill microorganisms (such as bacteria and viruses)
Attract pests (for example, to lure an insect or rodent to a trap).

Attractants (However, food is not considered a pesticide when used as an
attractant.)
Biopesticides are certain types of pesticides derived from such

Biopesticides
natural materials as animals, plants, bacteria, and certain minerals
Biocides Kill microorganisms
Disinfectants and Kill or inactivate disease-producing microorganisms on inanimate

sanitizers objects
Fungicides Kill fungi (including blights, mildews, molds, and rusts)
Fumigants Produce gas or vapor intended to destroy pests in buildings or soil
Herbicides Kill weeds and other plants that grow where they are not wanted
Insecticides Kill insects and other arthropods
Miticides Kill mites that feed on plants and animals
43 | P a g e
Microorganisms that kill, inhibit, or out compete pests, including

Microbial pesticides
insects or other microorganisms
Molluscicides Kill snails and slugs
Kill nematodes (microscopic, worm-like organisms that feed on

Nematicides
plant roots)
Ovicides Kill eggs of insects and mites
Pheromones Biochemicals used to disrupt the mating behavior of insects
Repellents Repel pests, including insects (such as mosquitoes) and birds
Rodenticides Control mice and other rodents
The impact of pesticides consists of the effects of pesticides on non-target species. Over 98% of

sprayed insecticides and 95% of herbicides reach a destination other than their target species,
because they are sprayed or spread across entire agricultural fields.
Runoff can carry pesticides into aquatic environments while wind can carry them to other fields,
grazing areas, human settlements and undeveloped areas, potentially affecting other species.
Other problems emerge from poor production, transport and storage practices. Over time,
repeated application increases pest resistance, while its effects on other species can facilitate the
pest's resurgence.
44 | P a g e
Each pesticide or pesticide class comes with a specific set of environmental concerns. Such
undesirable effects have led many pesticides to be banned, while regulations have limited and/or
reduced the use of others. Over time, pesticides have generally become less persistent and more
species-specific, reducing their environmental footprint. In addition the amounts of pesticides
applied per hectare have declined, in some cases by 99%. However, the global spread of
pesticide use, including the use of older/obsolete pesticides that have been banned in some
jurisdictions, has increased overall.
Specific pesticide effects
Pesticide environmental effects
Pesticide/class Effect(s)
Organochlorine DDT/DDE Egg shell thinning in raptorial birds
Endocrine disruptor
Thyroid disruption properties in rodents, birds,

amphibians and fish
Acute mortality attributed to inhibition of

acetylcholine esterase activity
DDT Carcinogen
Endocrine disruptor
45 | P a g e
Juvenile population decline and adult mortality in

DDT/Diclofol, Dieldrin and Toxaphene
wildlife reptiles
DDT/Toxaphene/Parathion Susceptibility to fungal infection
Earthworms became infected with monocystid

Triazine
gregarines
Chlordane Interact with vertebrate immune systems
Carbamates, the phenoxy herbicide 2,4-D,

Interact with vertebrate immune systems
and atrazine
Anticholinesterase Bird poisoning
Animal infections, disease outbreaks and higher

mortality.

Organophosphate
amphibians and fish
Oxidative damage
Modulation of signal transduction pathways
46 | P a g e
Impaired metabolic functions such

as thermoregulation, water and/or food intake and
behavior, impaired development, reduced
reproduction and hatching success in vertebrates.

Carbamate
amphibians and fish
Impaired metabolic functions such

as thermoregulation, water and/or food intake and
behavior, impaired development, reduced
reproduction and hatching success in vertebrates.
Interact with vertebrate immune systems
Acute mortality attributed to inhibition of

acetylcholine esterase activity
Phenoxy herbicide 2,4-D Interact with vertebrate immune systems
Atrazine Interact with vertebrate immune systems
Air
Pesticides can contribute to air pollution. Pesticide drift occurs when pesticides suspended in the
air as particles are carried by wind to other areas, potentially contaminating them. Pesticides that
are applied to crops can volatilize and may be blown by winds into nearby areas, potentially
47 | P a g e
posing a threat to wildlife. Weather conditions at the time of application as well as temperature
and relative humidity change the spread of the pesticide in the air. As wind velocity increases so
does the spray drift and exposure. Low relative humidity and high temperature result in more
spray evaporating. The amount of inhalable pesticides in the outdoor environment is therefore
often dependent on the season. Also, droplets of sprayed pesticides or particles from pesticides
applied as dusts may travel on the wind to other areas,or pesticides may adhere to particles that
blow in the wind, such as dust particles. Ground spraying produces less pesticide drift than aerial
spraying does.
Water
Pesticide residues have also been found in rain and groundwater. Pesticide impacts on aquatic
systems are often studied using a hydrology transport model to study movement and fate of
chemicals in rivers and streams. As early as the 1970s quantitative analysis of pesticide runoff
was conducted in order to predict amounts of pesticide that would reach surface waters.
There are four major routes through which pesticides reach the water: it may drift outside of the
intended area when it is sprayed, it may percolate, or leach, through the soil, it may be carried to
the water as runoff, or it may be spilled, for example accidentally or through neglect. They may
also be carried to water by eroding soil. Factors that affect a pesticide's ability to contaminate
water include its water solubility, the distance from an application site to a body of water,
weather, soil type, presence of a growing crop, and the method used to apply the chemical.
Soil
Many of the chemicals used in pesticides are persistent soil contaminants, whose impact may
endure for decades and adversely affect soil conservation.
The use of pesticides decreases the general biodiversity in the soil. Not using the chemicals
results in higher soil quality, with the additional effect that more organic matter in the soil allows
for higher water retention. This helps increase yields for farms in drought years, when organic
farms have had yields 20-40% higher than their conventional counterparts. A smaller content of
organic matter in the soil increases the amount of pesticide that will leave the area of application,
because organic matter binds to and helps break down pesticides.
48 | P a g e
Degradation and sorption are both factors which influence the persistence of pesticides in soil.
Depending on the chemical nature of the pesticide, such processes control directly the
transportation from soil to water, and in turn to air and our food. Breaking down organic
substances, degradation, involves interactions among microorganisms in the soil. Sorption
affects bioaccumulation of pesticides which are dependent on organic matter in the soil. Weak
organic acids have been shown to be weakly sorbed by soil, because of pH and mostly acidic
structure. Sorbed chemicals have been shown to be less accessible to microorganisms.
Effect on plants
Nitrogen fixation, which is required for the growth of higher plants, is hindered by pesticides in
soil.The insecticides DDT, methyl parathion, and especially pentachlorophenol have been shown
to interfere with legume-rhizobium chemical signaling. Reduction of this symbiotic chemical
signaling results in reduced nitrogen fixation and thus reduced crop yields. Root
nodule formation in these plants saves the world economy $10 billion in synthetic
nitrogen fertilizer every year.
Pesticides can kill bees and are strongly implicated in pollinator decline, the loss of species that
pollinate plants, including through the mechanism of Colony Collapse Disorder in which worker
bees from a beehive or western honey bee colony abruptly disappear. Application of pesticides to
crops that are in bloom can kill honeybees, which act as pollinators.
On the other side, pesticides have some direct harmful effect on plant including poor root hair
development, shoot yellowing and reduced plant growth.
Effect on animals
Many kinds of animals are harmed by pesticides, leading many countries to regulate pesticide
usage through Biodiversity Action Plans.
Animals including humans may be poisoned by pesticide residues that remain on food, for
example when wild animals enter sprayed fields or nearby areas shortly after spraying.
Pesticides can eliminate some animals' essential food sources, causing the animals to relocate,
change their diet or starve. Residues can travel up the food chain; for example, birds can be
harmed when they eat insects and worms that have consumed pesticides. Earthworms digest
49 | P a g e
organic matter and increase nutrient content in the top layer of soil. They protect human health
by ingesting decomposing litter and serving as bioindicators of soil activity. Pesticides have had
harmful effects on growth and reproduction on earthworms. Some pesticides can bioaccumulate,
or build up to toxic levels in the bodies of organisms that consume them over time, a
phenomenon that impacts species high on the food chain especially hard.
Birds
Reductions in bird populations have been found to be associated with times and areas in which
pesticides are used. DDE-induced egg shell thinning has especially affected European and North
American bird populations. In another example, some types of fungicides used in peanut farming
are only slightly toxic to birds and mammals, but may kill earthworms, which can in turn reduce
populations of the birds and mammals that feed on them.
Some pesticides come in granular form. Wildlife may eat the granules, mistaking them for grains
of food. A few granules of a pesticide may be enough to kill a small bird.
The herbicide paraquat, when sprayed onto bird eggs, causes growth abnormalities

in embryos and reduces the number of chicks that hatch successfully, but most herbicides do not
directly cause much harm to birds. Herbicides may endanger bird populations by reducing their
habitat.
Aquatic life
Fish and other aquatic biota may be harmed by pesticide-contaminated water. Pesticide surface
runoff into rivers and streams can be highly lethal to aquatic life, sometimes killing all the fish in
a particular stream.
Application of herbicides to bodies of water can cause fish kills when the dead plants decay and
consume the water's oxygen, suffocating the fish. Herbicides such as copper sulfite that are
applied to water to kill plants are toxic to fish and other water animals at concentrations similar
to those used to kill the plants. Repeated exposure to sublethal doses of some pesticides can
cause physiological and behavioral changes that reduce fish populations, such as abandonment of
nests and broods, decreased immunity to disease and decreased predator avoidance.
Application of herbicides to bodies of water can kill plants on which fish depend for their
habitat.
50 | P a g e
Pesticides can accumulate in bodies of water to levels that kill off zooplankton, the main source
of food for young fish. Pesticides can also kill off insects on which some fish feed, causing the
fish to travel farther in search of food and exposing them to greater risk from predators.
The faster a given pesticide breaks down in the environment, the less threat it poses to aquatic
life. Insecticides are typically more toxic to aquatic life than herbicides and fungicides.
Amphibians
In the past several decades, amphibian populations have declined across the world, for
unexplained reasons which are thought to be varied but of which pesticides may be a part.
Pesticide mixtures appear to have a cumulative toxic effect on frogs. Tadpoles from ponds

containing multiple pesticides take longer to metamorphose and are smaller when they do,
decreasing their ability to catch prey and avoid predators. Exposing tadpoles to
the organochloride endosulfan at levels likely to be found in habitats near fields sprayed with the
chemical kills the tadpoles and causes behavioral and growth abnormalities.
The herbicide atrazine can turn male frogs into hermaphrodites, decreasing their ability to

reproduce. Both reproductive and nonreproductive effects in aquatic reptiles and amphibians
have been reported. Crocodiles, many turtle species and some lizards lack sex-distinct
chromosomes until after fertilization during organogenesis, depending on temperature.
Embryonic exposure in turtles to various PCBs causes a sex reversal. Across the United States
and Canada disorders such as decreased hatching success, feminization, skin lesions, and other
developmental abnormalities have been reported.
Humans
Pesticides can enter the body through inhalation of aerosols, dust and vapor that contain
pesticides; through oral exposure by consuming food/water; and through skin exposure by direct
contact. Pesticides secrete into soils and groundwater which can end up in drinking water, and
pesticide spray can drift and pollute the air.
The effects of pesticides on human health depend on the toxicity of the chemical and the length
and magnitude of exposure. Farm workers and their families experience the greatest exposure to
agricultural pesticides through direct contact. Every human contains pesticides in their fat cells.
51 | P a g e
Children are more susceptible and sensitive to pesticides, because they are still developing and
have a weaker immune system than adults. Children may be more exposed due to their closer
proximity to the ground and tendency to put unfamiliar objects in their mouth. Hand to mouth
contact depends on the child's age, much like lead exposure. Children under the age of six
months are more apt to experience exposure from breast milk and inhalation of small particles.
Pesticides tracked into the home from family members increase the risk of exposure. Toxic
residue in food may contribute to a child’s exposure. The chemicals can bioaccumulate in the
body over time.
Exposure effects can range from mild skin irritation to birth defects, tumors, genetic changes,
blood and nerve disorders, endocrine disruption, coma or death. Developmental effects have
been associated with pesticides. Recent increases in childhood cancers in throughout North
America, such as leukemia, may be a result of somatic cell mutations. Insecticides targeted to
disrupt
Microbial Deterioration of Materials and types of Materials

Microbial deterioration is the decay or spoilage of any material as a result of the action
of bacteria, fungi or any other organism
Kinds of biodeterioration
Chemical biodeterioration
There are two modes of chemical biodeterioration. Both have a similar result, i.e. the material
becomes spoilt, damaged or unsafe, but the cause or biochemistry of the two is quite different:
● Biochemical assimilatory biodeterioration – the organism uses the material as food i.e. an
energy source.
● Biochemical dissimilatory biodeterioration – the chemical change in the food is as a result of
waste products from the organisms in question.
Physical biodeterioration
● Mechanical biodeterioration – this occurs when the material is physically disrupted/damaged
by the growth or activities of the organisms.
52 | P a g e
● Soiling/fouling – with this kind of biodeterioration the material or product is not necessarily
unsafe, but as its appearance has been compromised, it is rendered unacceptable. The building up
of biofilms on the surface of a material can affect the performance of that material.
The following points highlight ten economically important materials that are being deteriorated
by the activity of microorganisms.
The economically important materials are:
Pulp-Wood:
Pulp-wood represents the wood which is used to manufacture paper. It has been estimated that
almost about 10% of all the paper-wood cut is deteriorated by the action of microorganisms,
particularly fungi.
Temperature and moisture together with an appropriate availability of oxygen play an important
role in growing the fungi to deteriorate pulp-wood. Basidiomycetous fungi are responsible for
“white rots” and “brown rots” of pulp-wood. This classification of rots is based mainly upon the
constituent of the wood that is attacked.
If one finds white rotten patches on the pulp-wood surface, it characterizes the degradation of
brownish lignin leaving a white spongy cellulosic mass in the wood. Contrary to it, if there are
brown rotten patches, they are the result of preferential microbial deterioration of the cellulose
leaving behind a brown pinky mass predominantly of lignin.
When the moist pulp-wood is stored, its surface is attacked and degraded by some ascomycctous
and deuteromycetous fungi. This degradation is characteristically called “soft rots”.
Paper-Pulp:
As we know, the raw material, e.g., wood, cotton, linen rags, etc. are treated physically or
chemically for the purpose of separating and purifying cellulose fibrous in the form of fibrous
pulp. This pulp is generally called “paper-pulp”.
53 | P a g e
Those paper-pulps which are prepared by chemical treatments generally possess less nutrients for
microorganisms and hence are less susceptible to microbial attack than the physically
(mechanically) prepared paper-pulps.
However, microbial degradation of the paper-pulp may be encountered in the form of “paper-
pulp slime” spots on the finished paper sheet. Paper-pulp slime is produced by the deposition of
microorganisms and the subsequent enlargement of fibre, fines, and other debris from the water
and compounds of the paper-making medium.
Bacteria, yeasts, moulds, algae, and protozoa have been isolated from pulp slimes. Bacteria,
particularly capsulated bacilli such as Enterobacter aerogenes and Bacillus spp. represent the
most important group of pulp slime producers. Sphaerotilus natans, the filamentous iron
bacteria, can be found as part of the slime mass on those paper machines operating above pH 5.5.
The bacterium Alcaligenes viscosus var. dissimilis has been obtained from pink pulp slime.
Species of Mucor, Penicillium, Trichoderma, Fusarium, and yeasts (Torula, Rhodotorula) are the
fungi that have been isolated from pulp slimes in various paper-making industries.
Finished Paper:
Finished paper, i.e., the paper-sheet which is prepared by the refinement and fabrication of
paper-pulp is also attacked by microorganisms. Various fungi (Penicillium spp., Aspergillus spp.,
Chaetomium, etc.) and bacteria are the main attackers as cellulose, the main constituent of the
paper, is susceptible to them.
They may cause black, brown or yellow discoloration and spotting through “mildewing”. Glue or
casein, the other constituents of the paper, also serve as substrate for certain microorganisms.
This is the reason why some chemicals are generally added to the surface of the paper-sheet to
avoid microbial attack.
However, the microorganisms produce certain chemicals during their metabolism and these
chemicals cause staining or decolouration of the paper-sheet. Growth of cellulolytic
microorganisms may result in either weakening of fibres, perforations and/or even complete
destruction of the finished paper.
54 | P a g e
Textile and Cordage:
Textiles and cordages are susceptible to spoilage by certain microorganisms in raw, processing
and finished stages. Loss of millions of rupees is estimated annually due to attack of
microorganisms on these materials. The microorganisms involved in these deteriorations include
both bacteria and fungi.
Moulds are the principal microorganisms responsible for the deterioration of cellulose fibres
resulting in discolouration and weakening of fibre strength. The most important among bacteria
are the aerobic Bacillus spp., Proteus vulgaris, and some actinomycctes, whereas the most
important among fungi are Myrothecium verrucaria, Penicillium, Aspergillus, Alternaria,
Hormodendrum, Cladosporium, Fusarium, etc.
Moulds are essentially more important deteriorants of cotton textiles and their growth is favoured
by high humidity, moderate temperature and diminished light. The bacteria caused damage by
their proteolytic enzymes in woollen material which represents a protein, namely, keratin.
The nature of spoilage of textiles and cordages can be categorized as follows:

(i) Discolouration of fabric strain caused by pigment-producing (chromogenic bacteria) or
coloured spore-forming (dematiaceous fungi) microorganisms.
(ii) Loss of strength due to attack by microbial enzymes (Moulds on cotton fabrics and bacteria
on wool).
(iii) Change in the pH of the fibre resulting in change in shade of the dye.
Painted Surfaces:
Painted surfaces of the material are also subject to attack by microorganisms unless the paints
contain effective fungicidal ingredients. Painted surfaces exhibit evidence of mould-spotting or
discolouration under certain environmental conditions. This discolouration is due to products of
microbial metabolism of organic constituents of the paint.
Many moulds such as Aspergillus, Penicillium, Pullularia, Phomu glomerata, Alternaria, and
Cladosporium and a bacterium called Flavobacterium marinum have been isolated from
55 | P a g e
“mildewed” or “mouldy” painted surfaces. Pullularia spp. are considered to be the most common
cause of mould-spots on painted surfaces.
Rubber:
Rubber is subject to microbial deterioration, particularly natural rubbers rather than the synthetic
ones like neoprene. The deterioration is serious in electrical insulation of buried cables and in the
sealing rings of underground sewage pipes where the seals can decay long before the concrete
pipes themselves need replacing.
The organisms responsible are various fungi and actinomycetes. Some of the accelerators used in
the polymerization of rubber, such as dehydroabietyl ammonium pentachlorophenate, can help to
prevent decay because they have biocidal properties. To prevent this degradation some biocides
may be added during manufacture.
Leather:
We all know that several microorganisms harbour the living animals. When the animals die and
their skin is removed, the microorganisms continue to be present on the hides. When the hides
are taken for processing, several changes take place in the micro-flora.
If the leather or hide is preserved by drying and salting, most microorganisms are killed.
Contrary to it, if they are soaked in water to keep them soft, the microorganisms multiply
rapidly. Sometimes, undesirable microorganisms multiply and spoil the leather.
Besides, bacteria, some species of Aspergillus, Penicillium, Cladosporium, etc. are known to
attack the leather and cause hardening of it. The spoilage of leather goods is very common under
warm humid condition. On account of microbial attack, various types of leather goods are
deformed and spoiled.
Metal Corrosion:
Growth of several microbial species plays an important role in corrosion of metal pipes and
result in serious problem particularly in oil and gas delivery systems. Bacteria such as
Gallionella, Crenothrix, and Leptothrix species cause metal corrosion in aerobic conditions by
oxidizing metal and forming metallic oxides as corrosion products.
56 | P a g e
Thiobacillus species, the sulphur-oxidizing bacteria, produce high concentrations of sulphuric

acid in acrobic condition that causes corrosion. But, aerobic corrosion is not as serious as
anaerobic corrosion. Desulfovibrio desulfuricans, the sulphur-reducing bacterium, is especially
important in the corrosion of metals in anaerobic conditions by causing graphitization.
Graphitization is a process in which a metal-pipe losses much of its metal, becomes soft and
brittle, and easily broken. Anaerobic microbial corrosion of steel results in more localized pitting
which, sometimes, cause perforation of the pipe.
Wood Deterioration:
Forests are among the most valuable of all our resources as they provide us wood which is used
for various purposes.
The microorganisms cause decay of wood and there are two types of wood decay:
(i) destruction of lignin (or infrequently cellulose) resulting in white or spongy rotten wood. This
type of instruction is mainly caused by Tramets pini and Ganoderma applanatum, and
(ii) destruction of cellulose resulting in brown, soft and easily powdered wood. This destruction
is caused by Pliaeolus sp., Letinus lepideus, Serpula lacrymans, and Poria incrassata.
Food Spoilage:
Air-borne microorganisms such as fungal spores are often troublesome in our home and in
industries where food and food-products are manufactured.
Kinds of Organisms involved in Biodeterioration

Living organisms that can cause biodeterioration are referred to as biodeteriogens. Animals,
insects and higher plants can be easily identified by visual observation and by examining their
morphological and physiological characteristics. Organisms like bacteria, fungi and algae are
less easy to identify and need to be isolated to be examined. Growth of these organisms under
laboratory conditions is often difficult and specialized methods using fluorescent dyes and
antibodies or examination using a scanning electron microscope must be used. In some instances,
identification can only be made using DNA techniques.
57 | P a g e
Bacteria
Bacteria are a large diverse group of microscopic, prokaryotic, unicellular organisms. They can
be of various shapes (spherical, rod-like or spiral) and may be motile or non-motile. They
include both autotrophic and heterotrophic species, and can be aerobic or anaerobic, and many
species can thrive under either condition. They have relatively simple nutritional needs, and are
easily adaptable and can readily change to suit their environment.
Fungi
Fungi are a large group of small chemoheterotrophic organisms. They do not contain chlorophyll
and therefore cannot make their own food by using sunlight. They are, however extremely
adaptable and can utilize almost any organic material. Their growth is characterized by
unicellular or multicellular filamentous hyphae, which can often be the cause of physical
biodeterioration.
Algae, mosses and liverworts

Algae, mosses and liverworts are eukaryotic unicellular or multicellular organisms. They are
photoautotrophic and need moisture, light andinorganic nutrients to grow.
Higher plants
Higher plants are photoautotrophic organisms with specialized tissues and
organs that show functional specialization.
Insects
Insects include a large group of aerobic heterotrophic organisms. They need to feed on organic
matter, but as a group are diverse in what they can consume. They can feed off all processed and
unprocessed foods, as well as non-food items like binding materials and adhesives. Since some
insects are attracted to the tight, dark places that abound in storage areas, and since stored foods
and materials are handled infrequently, insects may do significant damage before they are
discovered. Some examples of insect pests are silverfish, psocids, cockroaches, borer beetles,
weevils and moths. Insects can be infected by disease-causing organisms such as bacteria,
58 | P a g e
viruses and fungi. Besides causing significant biodeterioration themselves, insects can
contaminate food or other organic matter.
Impact of Biodeterioration on the Environment

1. Eating deteriorated food caused by bacteria can cause food poison. .Food poisoning
occurs when you swallow food or water that has been contaminated with certain types of
bacteria, parasites, viruses, or toxins. Most cases of food poisoning are due to common
bacteria such as Staphylococcus, Escherichia coli (E. coli), Clostridium botulinum and
salmonella.
2. Biodeterioration of food and food materials on the field, in storage and during processing
can lead to food wastage and consequently loss of revenue and famine.
3. When industrial raw materials such as leather and pulp are biodeteriorated, it leads to
losses and consequently loss of job to many workers
4. Biodeterioration of building materials such as wood, will lead to a reduction in
quality/strength of the material.
Biodeterioration Control
Many materials are susceptible to deterioration by bacteria, fungi, insects and rodents. While a
few insects found among many materials may not incite great concern, certain conditions allow
pests to progress from grazing and perforation to complete destruction of materials.
1. Physical methods: e.g., drying (freeze drying) or cooling

2. Chemical/Biochemical methods such as adding biocide or preservative are effective
methods used to control biodeterioration.
3. Radiations such as gamma irradiation is a good control method.
4. Mechanical methods such as adhesive traps, pheromone traps, light traps, and mechanical
rodent traps capture pests and indicate where they are, thus allowing local control
measures to be taken.
59 | P a g e

1657 COURSES Soil Microbiology 3523

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

1657 COURSES Soil Microbiology 3523

Uploaded by

Copyright:

Available Formats

Lecture Note on Soil Microbiology By Mrs. Oyeyipo, F.M.

CHARACTERISTICS OF THE SOIL ENVIRONMENT

Soil Aggregates & Structure

Cation Exchange Capacity

The tendency of compounds to accept or donate electrons is expressed as “redox potential”.

SOIL TEXTURAL TRIANGLE

Soil Texture Triangle Activity

How to use the Soil Texture Triangle

(1) 60% clay, 20% silt, 20% sand Clay

SOIL MICROFLORA AND FAUNA AND THEIR ACTIVITIES

Soil fauna classification based on sizes

Meso and Microfauna

ASSOCIATION OF MICROORGANISMS WITH PLANT

Association with plant roots

Association with plant shoot

Association with plant litter

Biogeochemical cycle or substance turnover or cycling of substances is a pathway by which

The Carbon Cycle

Figure: The Carbon Cycle.

Ecosystems gain most of their carbon dioxide from the atmosphere. A number

Carbon is released from ecosystems as carbon dioxide gas by the process of respiration.

Carbon is stored in the lithosphere in both inorganic and organic forms. Inorganic deposits of

dioxide than agricultural land-use types.

The Nitrogen Cycle

The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into various

Figure: Nitrogen cycle

The processes of the nitrogen cycle

Atmospheric nitrogen must be processed, or "fixed", in a usable form to be taken up by plants.

 GS: Gln Synthetase (Cytosolic & Plastic)

Anaerobic ammonia oxidation

In this biological process, nitrite and ammonia are converted directly into

Figure: The water cycle

 First, water on the surface of the Earth evaporates.

Phosphorus Cycle on land

The phosphorus cycle is the biogeochemical cycle that describes the movement

The aquatic phosphorus cycle

Phosphorus occurs most abundantly in nature as part of the orthophosphate ion (PO4)3−,

The primary biological importance of phosphates is as a component of nucleotides, which serve

Process of the cycle

Mineral Transformation by Microorganisms

Microorganisms are intimately involved in mineral/metal biogeochemistry with a variety of

Biodegradation is the disintegration of materials by bacteria, fungi, or other biological means.

Biodegradable matter is generally organic material that serves as a nutrient for microorganisms.

substance frozen can prevent biodegradation. Most biodegradation occurs at temperatures

 halogenated organic solvents

Bioremediation technology exploits various naturally occurring mitigation processes: natural

Three primary ingredients for bioremediation are: 1) presence of a contaminant, 2) an electron

evolved. Petroleum hydrocarbons are naturally occurring chemicals; therefore, microorganisms

Microorganisms have limits of tolerance for particular environmental conditions, as well as

Temperature influences rate of biodegradation by controlling rate of enzymatic reactions within

Contaminants can adsorb to soil particles, rendering some contaminants unavailable to

In situ bioremediation causes minimal disturbance to the environment at the contamination site.

EFFECT OF PESTICIDES AND OTHER CHEMICALS IN THE ENVIRONMENT

The term pesticide includes all of the following: herbicide, insecticide, insect growth

In general, a pesticide is a chemical or biological agent (such as

Some examples of chemically-related pesticides are:

Organophosphates affect the nervous system by disrupting, acetylcholinesterase activity, the

terbacil, bispyribac-sodium, cyclosulfamuron, and pyrithiobac-

Microbial pesticides which consist of bacteria, entomopathogenic fungi or viruses (and

Classification based on type of pest

Pesticides that are related to the type of pests are:

Control algae in lakes, canals, swimming pools, water tanks, and

Kill or repel organisms that attach to underwater surfaces, such as