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

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 CO2 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.

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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

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https://microbewiki.kenyon.edu/index.php/File:Soilenv_figure1.jpeg

https://microbewiki.kenyon.edu/index.php/File:Soilenv_figure1.jpeg


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).

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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.

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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

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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

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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.

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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.

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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.)

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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

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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

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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.

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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

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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.

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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.

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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;

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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.

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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

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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

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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.

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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).

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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.

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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 (CO3-2) or bicarbonate

(HCO3-). Certain forms of sea life biologically fix bicarbonate with calcium (Ca+2) to

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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

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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.

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Figure: Nitrogen cycle

The processes of the nitrogen cycle

o 1 Nitrogen fixationo 2 Assimilationo 3 Ammonificationo 4 Nitrificationo 5 Denitrificationo 6 Anaerobic ammonia oxidationo 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

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https://en.wikipedia.org/wiki/File:The_Nitrogen_Cycle.png


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

bacteroids pass amino acids (with the newly fixed nitrogen) back to the plant, thus forming an

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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

blue-green algal populations. While not directly toxic to fish life, like ammonia, nitrate can have

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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 (N2), 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.

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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

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https://simple.wikipedia.org/wiki/File:Water_cycle.png


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

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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.

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https://en.wikipedia.org/wiki/File:Phoscycle-EPA.jpg


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.

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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

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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

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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

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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

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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

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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.

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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

(antimicrobial), 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

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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,

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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

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

other sites

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Antifouling agentsKill or repel organisms that attach to underwater surfaces, such as

boat bottoms

Antimicrobials Kill microorganisms (such as bacteria and viruses)

Attractants

Attract pests (for example, to lure an insect or rodent to a trap).

(However, food is not considered a pesticide when used as an

attractant.)

BiopesticidesBiopesticides are certain types of pesticides derived from such

natural materials as animals, plants, bacteria, and certain minerals

Biocides Kill microorganisms

Disinfectants and

sanitizers

Kill or inactivate disease-producing microorganisms on inanimate

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

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Microbial pesticidesMicroorganisms that kill, inhibit, or out compete pests, including

insects or other microorganisms

Molluscicides Kill snails and slugs

NematicidesKill nematodes (microscopic, worm-like organisms that feed on

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.

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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

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DDT/Diclofol, Dieldrin and ToxapheneJuvenile population decline and adult mortality in

wildlife reptiles

DDT/Toxaphene/Parathion Susceptibility to fungal infection

TriazineEarthworms became infected with monocystid

gregarines

Chlordane Interact with vertebrate immune systems

Carbamates, the phenoxy herbicide 2,4-D,

and atrazineInteract with vertebrate immune systems

Anticholinesterase Bird poisoning

Animal infections, disease outbreaks and higher

mortality.

OrganophosphateThyroid disruption properties in rodents, birds,

amphibians and fish

Oxidative damage

Modulation of signal transduction pathways

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Impaired metabolic functions such

as thermoregulation, water and/or food intake and

behavior, impaired development, reduced

reproduction and hatching success in vertebrates.

CarbamateThyroid disruption properties in rodents, birds,

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

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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.

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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

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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.

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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.

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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.

● 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.

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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”.

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.

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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.

Textile and Cordage:

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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

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“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.

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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.

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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,

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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.

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

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