Compiled MB 1

Agricultural
Microbiology By,
Sujan Kandel
Course outline
Agricultural Microbiology (ABE 211)
S.N. Topic No. of lecture
1. Introduction to microbiology and microorganisms
1.1 Evolution of microbial life; introduction, historical development,
scope and importance of microbiology; and practical application in
agriculture 1
1.2 Basic characteristics of prokaryotic and eukaryotic
microorganisms 1
2. Microbial nutrition and genetics
2.1 Nutritional requirements of bacteria and microbial growth curve 1
2.2 Genetics of bacteria: conjugation, transformation and transduction 1
Course outline
3. Role of microorganisms in soil fertility and crop production
3.1 Rhizosphere and phyllosphere effects and manipulation of rhizosphere
microflora to sustain plant productivity. 1
3.2 Factors influencing the activities of soil microorganisms and role of
microorganisms in formation of soil organic matter 1
4. Interrelationship between microorganisms and plants
4.1 Introduction to biological nitrogen fixation: symbiotic, associative and
non-symbiotic 1
4.2 Mechanism of root nodule formation and symbiotic nitrogen fixation in
legumes 1
4.3 Basic concept on phosphobacteria and mycorrhizae; microorganisms and
plant diseases with prime focus on signs and symptoms 1
Course outline
5. Biodegradation of agrochemicals and organic residues
5.1 Biodegradation of aliphatic compounds and aromatic compounds 1
5.2 Bioremediation: key concept, principle and process 1
5.3 Microbial degradation of organic residues (carbohydrates, proteins and fats) 1
6. Microorganisms involved in food products and food spoilage
(infections and toxins) and principle of food preservation 1
7. Alcohol fermentation and beverages; biogas, water purification and
effluent management and antibiotics 1
8. Biofertilizers: importance and mass production; biopesticides and
bioconversion of agricultural wastes for compost making 1
What is microbiology ?
“Study of microorganism or microbes”
•Microbiology is the study of living organisms of microscopic

size, which include bacteria, fungi, algae, protozoa and viruses. It
deals with their form, structure, reproduction, physiology,
metabolism and classification.
Characteristics of microorganisms:
• Their size is very small.
• There is no cellular differentiation.
• Microorganisms are present everywhere on the bodies

of animals and humans, on plant surfaces, in the air,
water, dust, soil, and even inside the intestinal canal of
all insects, birds, animals and human beings.
What are the types of microorganism?
Bacteria ▪ Cellular
Fungi ➢Unicellular or multicellular?
Actinomycetes ➢Prokaryotic or Eukaryotic?
Algae
Protozoa
Nematodes ▪ Acellular
Helminths
Viruses
Distribution of Microorganism
Air Water
Environment
Microorganisms Nature
Food Soil
Sub-disciplinesof microbiology
• General Microbiology:
• Medical Microbiology: studies microbes that
cause human disease
• Immunology: studies about microbes and immune
system.
• Agricultural microbiology:
• Microbial ecology: studies about microbes and their
habit, habitat.
• Food microbiology: studies about microbes on food
and food borne disease, microbes used on food and
beverages.
• Industrial microbiology: studies about
commercially utilized microbes.
• Biotechnology
• Diary Microbiology etc.
Historical Background and Development
➢ History:
➢ A. Discovering the "organisms”:
1. 1676: A. Leeuwenhoek – first to observe and describe microbes accurately
2. 1884: C. Chamberland – constructed a bacterial filter that allowed the
identification of viruses
3. 1898: Loeffler and Frosch – identified filterable infectious agent as cause of
foot-and-mouth disease in cattle
4. 1898-1900: M. Beijerinck – identified tobacco mosaic virus
5. 1982: S. Prusiner – described prions (infectious protein that causes a
particular normal protein to alter its shape and become a prion)
➢ B. Disproving spontaneous generation (that living organisms could develop from nonliving
matter):
1. 1688: F. Redi – first to challenge theory of spontaneous generation by showing that if raw meat was
protected from flies, the formation of maggots was prevented
2. 1748: R. Needham – supported spontaneous generation of microbes by showing that even after
boiling mutton broth and pouring into sealed containers, growth of microbes occurred
3. 1776: L. Spallanzani - challenged spontaneous generation as it pertained to microbes by showing that
sealed containers that were boiled do not produce microbes
4. 1861: L. Pasteur – rigorously disproved spontaneous generation
a) filtered air showed that air contained microbial organisms
b) constructed flasks with curved neck that allowed air into the flasks while
➢ dust, etc. remained in the neck placed broth into the flasks and boiled
➢ showed that no microbial growth resulted unless flasks were tipped to allow the broth into the
neck
➢ C.The germ theory of disease:
1. Previously, people thought that disease was punishment for an individual's crimes, due to
poisonous vapors.
2. The idea that invisible organisms caused disease were given by Lucretius and Fracastoro
(1546).
3. 1835: A. Bassi showed that silkworm disease was due to a fungus.
4. 1867: J. Lister showed that antiseptic surgical procedures reduced the frequency of wound
infections.
5. 1876/1884: R. Koch definitively proved that Bacillus anthracis caused the disease anthrax in cows
and Mycobacterium tuberculosis caused the disease tuberculosis using Koch's postulates:
a) The suspected pathogen should be present in ALL cases of the disease and NOT present in
healthy animals.
b) The suspected pathogen should be grown in vitro in pure culture.
c) Cells from a pure culture of the putative pathogen should cause disease in healthy animals.
d) The putative pathogen should be re-isolated from the infected animal.
D. Preventing disease by vaccination:
1. E. Jenner inoculated people with cowpox to protect against smallpox.
2. 1885 – Pasteur developed the rabies vaccine.
3. 1890: von Behring and Kitasato produced antibodies to purified toxins to
protect against diphtheria and tetanus.
4. 1884: E. Metchnikoff described phagocytosis of bacteria.
E.Discovering the effect of microbes on organic and inorganic

matter:
1. 1856: Pasteur described lactic acid fermentation; contributions to wine
industry.
2. 1887-1900: S.Winogradsky and M. Beijerinck studied soil microbes and
their role in the biochemical cycles of sulfur, carbon, nitrogen
Recent history of microbiology (the 20th century)
A. Infectious diseases: The etiological agent of most infectious diseases has been
ascertained. Current research focuses on understanding the molecular mechanisms by
which disease is caused.
B. Chemotherapy: Discovery of antibiotics; antibiotic resistance
C. Immunology develops as a science.
D. Physiology and biochemistry: Using microbes as a model, many
physiological and biochemical processes have been elucidated.
E. Genetics: Many of the advances in molecular genetics were made using bacteria as
models.A few of the many:
1.1941: Beadle and Tatum – 1 gene = 1 enzyme
2.1943: Luria and Delbruck – mutations are spontaneous in nature
3.1944: Avery, MacLeod, and McCarty – DNA is the genetic material
4.1961: Jacob and Monod – the operon and gene regulation
Recent history of microbiology (the 20th century)
F.Molecular biology:
➢ Many of the advances in molecular biology were made using
bacteria as models.A few of the many:
1. 1970: Restriction enzymes discovered
2. 1979: Insulin synthesized using recombinant techniques
3. 1990: Gene therapy trials begin
4. 1995:The nucleotide sequence of the first free-living organism
(Haemophilus influenzea) published
Scope of Microbiology
Microbiology
1. Agricultural Microbiology/ soil Microbiology:
➢ Microorganisms related to soil fertility, plant diseases, transformation
of matter, biological nitrogen fixations etc are studied.
2. Food Microbiology:
➢ Microorganisms important with respect to food viz., food
fermentations, food spoilage, food poisoning and food preservation are
studied in this area.
3. Industrial Microbiology:
➢ Microbial production of useful products like antibiotics, fermented
beverages, alcohols, industrial chemicals, organic acids, enzymes,
hormones etc are studied in this area.
4. Medical Microbiology:
Besides their usefulness, microorganisms are casual agents of several diseases
of plants, animals and human beings. Many diseases are caused by viruses also.
Medical Microbiology deals with studies on causative agents of disease,
diagnostic procedures, identification of disease-causing organisms, development
of effective vaccines and preventive measures etc.
5. Exo-Microbiology:
It deals with exploration of existence of biomolecules and microbial life in
outer space.
6. Geochemical Microbiology:
Prospects for deposits of coal, mineral and gas, recovery of minerals from low
grade ores, sea water mining operations, coal, mineral and gas formation and
exploration are studied in this area.
7. Molecular Biology:
➢ It is the program of interpreting the specific structure and function of organisms
in terms of their molecular structures. Microorganisms have been used as a tool
to explore fundamental life processes because of many advantages; their fast rate
of reproduction, their growth can be easily manipulated, and lysed cells can be
studied in terms of specific chemical reactions, specific products and specific
structures involved.
8.Genetic engineering and Biotechnology:
➢ This is an important development in applied Molecular Biology which refers to
the human capability to alter the genetic make up of an organism. It has been
possible because of the detailed knowledge of structure and function of DNA
and discovery of the restriction enzymes which can cleave or cut the DNA at
specific sites along the chain length. Use of genetically engineered
microorganisms has opened great potential for production of drugs, vaccines,
improvement of agricultural crops etc.
9. Environmental Microbiology:
➢ It deals with use of microorganisms to protect the environment from
the toxic pollutants, reduction of microbial load in the sewage and
industrial wastes, pesticides, insecticides, heavy metals etc. and to
develop suitable methods for treatment of these wastes and their
recycled use.
Application of microorganism
Microorganisms play an important role in sustaining life
on this planet and in our daily life through the following activities:
1. Transformation of matter:
Microorganisms degrade dead organic matter and return to the atmosphere
in inorganic form. They complete the cycle of matter and are responsible
for transformation of C, N and S and other important elements which are
essential for life.
2.Biological nitrogen fixation:
They fix nitrogen from atmosphere and make it available to the plants in
usable form. Important microorganisms under this category include,
Rhizobium, Azotobacter, Azospirillum etc.
3.Mycorrhiza:
➢ Association of roots of many plants with fungi forms a composite structure called
mycorrhiza. Fungus helps in absorption of mineral salts from soil and plant in turn provides
carbohydrates for the growth of fungus.
4.Silage:
➢ This method is used to preserve feed with its characteristic flavor, taste and nutritive value.
Leaves of green plants are compacted in size and some molasses is added. Lactic acid
bacteria develop and produce lactic acid which helps to conserve the cattle feed.
5.Cellulose degradation in Rumen:
➢ Ruminants feed on straw and grass which contains about 50 % cellulose. There is symbiotic
association of microorganisms with rumen for degradation of cellulose and about 1010 – 10
11 cells/ml of different bacteria are usually present in the rumen. Most important of these
include Ruminococcus and Clostridium.

6.Biogas:
➢ Animal waste products and cellulose containing waste is fermented by
microorganisms (Methanogens). Animal excreta is preserved in rotting sediment and
methane gas so formed is used as a fuel.
7.Composting:
➢ Decomposition of organic matter by microorganisms to convert it into nutrient rich
manure is known as composting. Bacillus, Aspergillus and Thermoactinomyces are
important in this process.
8.Industrial uses:
➢ Different microorganisms are used for the production of wide range of products
at industrial scale. These include alcoholic beverages, antibiotics, enzymes,
pharmaceuticals etc.
Importance of microbiology in Agriculture
• Involved in nutrient transformation process

• Decomposition of resistant components of plant and animal tissue
• Role in microbial antagonism
• Participate in humus formation
• Predator to nematodes
• Improves soil structure
• Maintenance of biological equilibrium
• Use in biofertilizers.
• Use in dairy industries.
PROKARYOTIC & EUKARYOTIC
MICROORGANISMS
Prokaryotic Microorganism
Pro = before (primitive)

Karyon = nucleus
➢ Any Cellular organism that has no nuclear membrane, no organelles in the
cytoplasm except ribosome and has its genetic materials in the form of
single continuous strands forming coil or loops is known as Prokaryotic
Microorganism.
➢ Most prokaryotes are unicellular organisms, although a few such as
myxobacteria have multicellular stages in their life cycles.
• Prokaryotes are the single-celled organisms and much smaller than eukaryotic cells.
• The size of most prokaryotes is between 1 µm and 10 µm but can vary in size from
0.2 µm to 750 µm.
• The prokaryotes are divided into two domains:
1. the bacteria, unicellular microorganisms that have wide range of shapes and
ubiquitous in habitat ,
2. the archaea (e.g Halobacteria), single-celled prokaryotic microorganisms similar
to bacteria but possess some genes and several metabolic pathways that are closely
related to those of eukaryotes.
• Exists in different shapes like, coccus, bacillus, spirillum, coccobacillus, and spirochete.
While some of the prokaryotes are pleomorphic i.e. do not possess constant shape
and some exists as aggregate communities.
Structure and Reproduction of Prokaryotes
• Prokaryotic cell contains Flagellum, cell wall (absent in Mycoplasma), cell
membrane, cytoplasm, ribosome, nucleiod, glycocalyx, and inclusion
bodies.
• Membrane bound organelles like mitochondria, chloroplast, nucleus, etc.
are absent in prokaryotes.
• Genetic material of prokaryotes is not present in nucleus and consists of a
large DNA molecule compacted in an area of cytoplasm called the
nucleiod region.
• Cell wall of the prokaryotes is composed of peptidoglycan, a single large
polymer of amino acids and sugar.
• Some of the prokaryotes produce endospores during extreme conditions.
• Locomotion is through flagella.
• Pilus when present helps in adherance.
• Capsule, a bacterial glycocalyx protects from host defenses and contributes to the
pathogenicity.
• Prokaryotes live in nearly all environments even in harsh conditions such as high
temperature and high salinity.
• Some species contain protein-enclosed microcompartments like
carboxysomes or gas vacuoles that distinct physiological roles.
• Prokaryotes are asexual and usually reproduction is by binary fission or budding.
Genetic exchange and recombination occur in the form of horizontal gene transfer
and is not a replicative process as in eukaryotes.
• Prokaryotes have a larger surface-area-to-volume ratio giving them a higher
metabolic rate, a higher growth rate and therefore a shorter generation time
compared to Eukaryotes
• Appandages
➢ Pili
• straight hair like appendages;
• they are usually short;
• all gram-negative bacteria have pili;
• function is to attach bacteria to other bacteria, other cells, or other surfaces
(not for locomotion):
• Appandages
➢Flagella (singular – flagellum)

• long, thin structures that extend outward from the surface of the envelope;
• function is locomotion - bacteria with flagella are motile;
• Bacteria can have 1, 2, or many flagella (ex. of a bacteria with many
flagella – Salmonella).
➢Flagella & Pilli
Prokaryotic fission
Significance of Prokaryotes
➢Prokaryotes continue to have an enormous ecological impact.
➢Prokaryotes, along with fungi, are decomposers that recycle chemical

elements in ecosystems.
➢Some prokaryotes live with other species in symbiotic relationships.
➢Some parasitic prokaryotes are pathogenic, causing disease in the host.
➢Bacteria have been put to work in laboratories, sewage treatment

plants, and the food and drug industry.
PROKARYOTIC &
EUKARYOTIC
MICROORGANISMS
Pro = before (primitive)

Karyon = nucleus
➢ Any Cellular organism that has no nuclear membrane, no organelles in
the cytoplasm except ribosome and has its genetic materials in the form
of single continuous strands forming coil or loops is known as
Prokaryotic Microorganism.
➢ Most prokaryotes are unicellular organisms, although a few such as
myxobacteria have multicellular stages in their life cycles.
• Prokaryotes are the single-celled organisms and much smaller than

eukaryotic cells.
• The size of most prokaryotes is between 1 µm and 10 µm but can vary
in size from 0.2 µm to 750 µm.
• The prokaryotes are divided into two domains:
1. the bacteria, unicellular microorganisms that have wide range of
shapes and ubiquitous in habitat
2. the archaea (e.g Halobacteria), single-celled prokaryotic
microorganisms similar to bacteria but possess some genes and several
metabolic pathways that are closely related to those of eukaryotes.
• Exists in different shapes like,
coccus, bacillus, spirillum,
coccobacillus, and spirochete.
While some of the prokaryotes
are pleomorphic i.e. do not
possess constant shape and
some exists as aggregate
communities.
Structure of Prokaryotes
• Prokaryotic cell contains Flagellum, cell wall (absent in Mycoplasma), cell
membrane, cytoplasm, ribosome, nucleiod, glycocalyx, and inclusion
bodies.
• Membrane bound organelles like mitochondria, chloroplast, nucleus, etc.
are absent in prokaryotes.
• Genetic material of prokaryotes is not present in nucleus and consists of a
large DNA molecule compacted in an area of cytoplasm called the
nucleiod region.
• Cell wall of the prokaryotes is composed of peptidoglycan, a single large
polymer of amino acids and sugar.
• Some of the prokaryotes produce endospores during extreme conditions.
Structure of Prokaryotes
• Locomotion is through flagella.
• Pilus when present helps in adherence.
• Capsule, a bacterial glycocalyx protects from host defenses and contributes to the
pathogenicity.
• Prokaryotes live in nearly all environments even in harsh conditions such as high
temperature and high salinity.
• Some species contain protein-enclosed microcompartments like
carboxysomes or gas vacuoles that distinct physiological roles.
• Prokaryotes are asexual and usually reproduction is by binary fission or budding.
Genetic exchange and recombination occur in the form of horizontal gene transfer
and is not a replicative process as in eukaryotes.
• Prokaryotes have a larger surface-area-to-volume ratio giving them a higher
metabolic rate, a higher growth rate and therefore a shorter generation time
compared to Eukaryotes
➢Flagella & Pilli
• Appendages
➢ Pili
• straight hair like appendages;
• they are usually short;
• all gram-negative bacteria have pili;
• function is to attach bacteria to other bacteria, other cells, or other surfaces (not
for locomotion)
➢Flagella (singular – flagellum)
• long, thin structures that extend outward from the surface of the envelope;
• function is locomotion - bacteria with flagella are motile;
• Bacteria can have 1, 2, or many flagella (ex. of a bacteria with many flagella –
Salmonella).
Structure of Prokaryotic Microorganisms
Prokaryotic cells are not as complex as eukaryotic cells. Using bacteria as our sample
prokaryote, the following structures can be found in bacterial cells:
Internal Structures of Prokaryotic Cells:
1. Plasma Membrane:
The plasma membrane is a double-layer of phospholipids
with associated proteins and other molecules. The lipids
occur in two layers (a bilayer). Proteins embedded in the
bilayer appear to float within the lipid, so the membrane is
constantly in flux. The membrane is therefore referred to as
a fluid mosaic structure. Within the fluid mosaic structure,
proteins carry out most of the membrane's functions. It is
essentially the bag that holds all of the intracellular material
and regulates the movement of materials into and out of
the cell.
Internal Structure of Prokaryotic Microorganisms
2. Cytoplasm:
➢ The cytoplasm in prokaryotic cells is a gel-like substance in which all of the
other cellular components are suspended. It is very similar to the eukaryotic
cytoplasm, except that it does not contain organelles. Recently, biologists
have discovered that prokaryotic cells have a complex and functional
cytoskeleton similar to that seen in eukaryotic cells.
3. Cytoskeleton:
➢ It's only recently been discovered that rod-shaped bacteria and Archaea possess
cytoskeletal proteins that function in a similar way to the cytoskeleton of eukaryotic
cells. cytoskeleton is an interconnected system of fibers, threads, and interwoven
molecules that give structure to the cell. The main components of the cytoskeleton
are microtubules, microfilaments, and intermediate filaments. All are assembled
from subunits of protein. This scaffolding provides structural support to the cell
and plays a role in cell-division.
4. Ribosomes:
➢ Ribosomes in prokaryotes are smaller than eukaryotes. It consists 70s type
ribosome. These ribosomes possess two subunits : one smaller which is 30s in
nature and next larger one which is 50s in nature. Ribosomes are the protein-
making machinery of the cell.
5. Genetic Material of Prokaryotes:
➢ All prokaryotic cells contain large quantities of genetic material in the form of
DNA and RNA. The DNA tends to look like a mess of string in the middle of the
cell.
a.Nucleoid:
➢ The nucleoid is the region of the prokaryotic cytoplasm that contains the genome—
the main genetic material (DNA) of the cell. Bacteria and Archaeans typically have a
single, circular chromosome.
5. Genetic Material of Prokaryotes:

b.Plasmids:
➢ In addition to the bacterial chromosome, bacteria may also contain one or more
plasmids. A plasmid is a non-essential piece of DNA that confers an advantage to the
bacteria, such as antibiotic resistance, virulence (the ability to cause disease) and
conjugation (a bacterium’s ability to share its plasmids with other bacteria). Plasmids
are also found in some eukaryotic microbes, such as yeasts.
External Structure of Prokaryotic Microorganisms
1. Cell wall:
➢ It surrounds some cells and gives them shape and rigidity.
➢ It is located outside the cell membrane and prevents osmotic lysis (bursting due to
increasing volume).
➢ The composition of cell walls vary depending on the type of organisms, but most cell
walls contain a combination of the major organic molecules—proteins, carbohydrates
and lipids.
➢ Bacteria have a unique molecule called peptidoglycan in their cell wall.
➢ Cell wall composition of bacteria allow scientists to classify them as
either Gram-positive or Gram-negative.
External Structure of Prokaryotic Microorganisms
2. Glycocalyx:
➢ The glycocalyx is a layer present in some bacteria, and located outside of the cell wall.
There are two types of glycocalyces: slime layers and capsules. Slime layers
help bacteria stick to things and protect them from drying out, particularly in
hypertonic environments. Capsules also allow bacteria to stick to things, but have
the added benefit of helping encapsulated bacteria hide from the hosts immune
system.
3. Flagella
4. Pili
Prokaryotic fission
Bacteria are divided into two major groups: gram-positive
and gram- negative, based on their reaction to gram staining:
Comparison of prokaryotic and eukaryotic cell
Significance of Prokaryotes
➢Prokaryotes continue to have an enormous ecological impact.
➢Prokaryotes, along with fungi, are decomposers that recycle chemical

elements in ecosystems.
➢Some prokaryotes live with other species in symbiotic relationships.
➢Some parasitic prokaryotes are pathogenic, causing disease in the host.
➢Bacteria have been put to work in laboratories, sewage treatment

plants, and the food and drug industry.
Eukaryotic Microorganisms
➢ The word Eukaryote comes from the Greek word Eu and karyon Eu = Well (true)
➢ Karyon = nucleus
➢ A single-celled or multicellular organism whose cells contain a distinct membrane-
bound nucleus.
➢ A eukaryote is any organism whose cells contain a nucleus and other structures
(organelles) enclosed within membranes.
➢ The defining membrane-bound structure that sets eukaryotic cells apart from
prokaryotic cells is the nucleus, or nuclear envelope, within which the genetic material is
carried.
➢ Most eukaryotic cells also contain other membrane-bound organelles such as
mitochondria or the Golgi apparatus.
➢ In addition, plants and algae contain chloroplasts.
➢ Many unicellular organisms are eukaryotes, such as protozoa. All multicellular organisms
are eukaryotes, including animals, plants and fungi.
Examples of Eukaryotic Microorganisms
• Rhizopus
• Amanita
• R. arrhizus
• Acaulospora,
• Aspergillus
• Entrophospora,
• Penicillium
• Gigaspora,
• Giardia lamblia
• Glomus,
• Entamoeba histolytica
• Sclerocystis
• Plasmodium
• Scutellospora
• Saccharomyces cerevisiae
• Lactarius
• Candida albicans
NUTRITIONAL REQUIREMENT
& GENETICS OF BACTERIA
Nutritional types of Bacteria
➢ Bacteria require sources of carbon, nitrogen, phosphorous, iron and a large
number of other minerals. Carbon, nitrogen and water are used in highest
quantities.
➢ The nutritional requirements for bacteria can be grouped according to the
carbon source and the energy source:
1. Autotrophs:
• Autotrophs are bacteria which obtain their nutrition from inorganic
compounds.
• Carbon dioxide is typically the sole source of cellular carbon.
• Autotrophs will use hydrogen sulfide, ammonia or hydrogen gas to reduce
carbon into necessary sugars.
• Nitrifying bacteria, which oxidize ammonia to create nitrites and nitrates, are
an example of bacteria which use autotrophic nutrition.
2. Heterotrophs:
➢ Bacteria that require organic sources of carbon such as sugars, fats and amino
acids are termed heterotrophs.
➢ Saprophytic bacteria are an example. They attain their nutrition from dead
organic matter.
➢ Using enzymes, these bacteria will break down complex compounds and use the
nutrients to release energy.
➢ Saprophytic bacteria are essentially decomposers and play an important role in
ecosystem by releasing simpler products which plants and animals can use.
3. Phototrophs:
➢ Phototrophic bacteria absorb light energy, then utilize this in photosynthesis to
create cellular energy.
➢ There are two types of phototrophs; those which do not produce oxygen as a
byproduct are termed anaerobic phototrophs, while those which do produce
oxygen are termed aerobic phototrophs.
➢ Both autotrophs and heterotrophs can be phototrophs. Cyanobacteria are an
example of bacteria which execute photoautotrophic nutrition.
4. Chemotrophs:
➢ These bacteria obtain chemical energy from their surroundings
and convert it into adenosine triphosphate (ATP) for cellular use.
➢ Chemotrophs attain energy from oxidation-reduction reactions of
inorganic compounds such ammonia, hydrogen sulfide and iron.
➢ For instance, sulfur bacteria is a chemoautotroph which produces energy
by oxidizing hydrogen sulfide into sulfur and water.
5. Lithotrophs:
➢ Lithotrophs are bacteria which use reduced inorganic compounds as
the electron donor (H-donor) in anaerobic or aerobic respiration.
Nutritional Requirement of Bacteria
There are basically three groups of nutrients required for normal bacterial growth:
1. Mineral Nutrient
2. organic Nutrient
3. Growth Factors
1. Mineral Nutrients:
• Mineral nutrients are also known as inorganic nutrients.
• On the requirements of mineral nutrients, these are further grouped into:
a. Major Nutrients: C, H, O, N, P, K, S & Mg
b. Minor Nutrients: Ca, Mn, Zn, Cu, Fe, Mo.
➢ Water is also major requirements which constituents important part of the cell.
➢ Nitrates, Nitrites and organic nitrogenous compound like amino acids, nucleic acids,
peptides, peptones, proteins etc provides source of N to bacteria.
➢ P & S are also required for bacteria.
Nutritional Requirement of Bacteria
2. Organic Nutrients:
➢ Dead and decayed bodies of living organisms provides organic substances to the bacteria.
➢ Carbohydrates, proteins, fats, nucleic acids, are common organic nutrients
➢ Bacteria and other microorganisms derived their energy from degradation products of
Carbohydrates, proteins, fats, nucleic acids.
3. Growth Factors:
➢ Most bacteria are able to produce growth factors by themselves.
➢ Those which do not synthesize important growth factors, additional supplements of these
growth factors is important.
➢ The important growth factors are:
➢ Vitamins (Thiamine. Niacin, Pyridoxin, Riboflavin, Nicotinic acids , biotin etc)
➢ p-Amino benzoic acid
➢ Inositol, Folic acids, Lipoic acids
Bacterial Growth Curve
Generation time
➢ The time in which population of microorganism doubles.

➢ So, it is also called as doubling time
➢ Generation time of E. coli is 20 min
➢ Generation time g = t/n
Genetics of Bacteria (Recombination Mechanism)
➢ Bacteria reproduce by the process of binary fission.

➢ In this process, the chromosome in the mother cell is replicated and a copy is
allocated to each of the daughter cells.
➢ As a result, the two daughter cells are genetically identical.
➢ Several events occur that change the bacterial chromosome and then these changes
are passed on to future generations by binary fission.
Reproduction in Bacteria
➢ Transverse binary fission

➢ Fragmentation
➢ Spore Production
➢ Budding
Recombination
Recombination:
➢ Geneticrecombination refers to the exchange between two DNA molecules.
– It results in new combinations of genes on the chromosome.
– In crossing over, two homologous chromosomes (chromosomes that contain the
same sequence of genes but can have different alleles) break at corresponding
points, switch fragments and rejoin.
– The result is two recombinant chromosomes.
➢ In bacteria, crossing over involves a chromosome segment entering the cell and
aligning with its homologous segment on the bacterial chromosome.
➢ The two break at corresponding point, switch fragments and rejoin.
➢ The result, as before, is two recombinant chromosomes and the bacteria can be called
a recombinant cell.
Genetic Transfer
➢ Genetic transfer is the mechanism by which DNA is transferred from a donor to a

recipient.
➢ Once donor DNA is inside the recipient, crossing over can occur.
– The result is a recombinant cell that has a genome different from either the donor
or the recipient.
➢ In bacteria genetic transfer can happen by three ways:
– Transformation
– Transduction
– Conjugation
Transformation
➢ It is a process in which free DNA is taken up by a cell, resulting in a genotypic change
in the recipient.
➢ After death or cell lyses, some bacteria release their DNA into the
environment.
➢ Other bacteria, generally of the same species, can come into contact with these
fragments, take them up and incorporate them into their DNA by recombination.
➢ This method of transfer is the process of transformation.
➢ Any DNA that is not integrated into the chromosome will be degraded.
➢ The genetically transformed cell is called a recombinant cell because it has a different
genetic makeup than the donor and the recipient.
➢ All of the descendants of the recombinant cell will be identical to it.
➢ In this way, recombination can give rise to genetic diversity in the population.
Transformation
Griffith's Experiment:
➢ The transformation process was first demonstrated in 1928 by Frederick Griffith.
➢ Griffith experimented on Streptococcus pneumoniae, a bacteria that causes pneumonia in mammals.
➢ When he examined colonies of the bacteria on petri plates, he could tell that there were two different
strains.
– The colonies of one strain appeared smooth.
• Later analysis revealed that this strain has a polysaccharide capsule and is virulent, that it, it
causes pneumonia.
– The colonies of the other strain appeared rough.
• This strain has no capsules and is avirulent.
➢ When Griffith injected living encapsulated cells into a mouse, the mouse died of pneumonia and
the colonies of encapsulated cells were isolated from the blood of the mouse.
➢ When living nonencapsulated cells were injected into a mouse, the mouse remained healthy
and the colonies of nonencapsulated cells were isolated from the blood of the mouse.
Transformation
➢ Griffith then heat killed the encapsulated cells and injected them
into a mouse.
• The mouse remained healthy, and no colonies were isolated.
• The encapsulated cells lost the ability to cause the disease.
➢ However, a combination of heat-killed encapsulated cells and living
nonencapsulated cells did cause pneumonia and the mouse died and
colonies of living encapsulated cells were isolated from the mouse.
➢ How can a combination of these two strains cause pneumonia when
either strand alone does not cause the disease?
Transformation
• If you guessed the process of transformation, you are right!
➢ The living nonencapsulated cells came into contact with DNA fragments of the
dead capsulated cells.
➢ The genes that code for the capsule entered some of the living cells and a
crossing over event occurred.
➢ The recombinant cell now has the ability to form a capsule and cause
pneumonia.
➢ All of the recombinant's offspring have the same ability.
➢ That is why the mouse developed pneumonia and died.
Transformation
➢ Bacterial transformation has been demonstrated in several bacteria. For

e.g.: Bacillus subtilis, Haemophilus influenzae, Rhizobium, E. coli, Streptococcus
and Streptomyces.
➢ The process of transformation in all these organisms has certain
common features:
▪ The purified donor DNA is first transported across the cell membrane
into the recipient ―Component cells‖ (Cell that can take of DNA)
▪ The DNA undergoes recombination with the recipient DNA and is
then expressed.
Conjugation
➢ A second mechanism by which genetic transfer takes place is conjugation.

➢ Conjugation in bacteria is a mechanism for gene transfer that
requires cell-to-cell contact.
➢ This mechanism requires the presence of a special plasmid called the F
plasmid.
Conjugation
Therefore, we will briefly review plamid structure before continuing.

➢ Plasmids are small, circular pieces of DNA that are separate and replicate
independently from the bacterial chromosome.
➢ Plasmids contain only a few genes that are usually not needed for growth and
reproduction of the cell.
➢ However, in stressful situations, plasmids can be crucial for survival.
➢ The F plasmid, for example, facilitates conjugation.
• This can give a bacterium new genes that may help it survive in a changing
environment.
➢ Some plasmids can integrate reversibly into the bacterial chromosome.
• Such plasmid which has capacity of integrations called an episome.
Conjugation
➢ Bacteria that have a F plasmid are referred to as F+ or male.
• Those that do not have an F plasmid are F- of female.
➢ The F plasmid consists of 25 genes that mostly code for production of sex pili.
➢ A conjugation event occurs when the male cell extends his sex pili, and one attaches to
the female.
• This attached pilus is a temporary cytoplasmic bridge through which a replicating F
plasmid is transferred from the male to the female.
• When transfer is complete, the result is two male cells.
➢ This F plasmid can behave as an episome.
• When the F+ plasmid is integrated within the bacterial chromosome, the cell is
called an Hfr cell (high frequency of recombination cell).
• The F plasmid always inserts at the same spot for a bacterial species.
Conjugation
➢ The Hfr cell still behaves as a F+ cell, transferring F genes to a F-cell, but now it can
take some of the bacterial chromosome with it.
➢ Replication of the Hfr chromosome begins at a fixed point within the F episome and
the chromosome is transferred to the female as it replicates.
➢ Movement of the bacteria usually disrupts conjugation before the entire
chromosome, including the tail of the F episome can be transferred.
– Therefore, the recipient remains F- because the F plasmid is not entirely
transferred.
➢ A cross over event can occur between homologous genes on the Hfr fragment
and the F- DNA.
➢ Pieces of DNA not recombined will be degraded or lost in cell division.
➢ Now the recombinant genome can be passed on to future generations.
Fig: Conjugation in Bacteria (F+ x F- Cross)
Transduction
➢ Transduction is a process in which bacterial DNA is transferred from one cell to
another with the help of a virus.
➢ This method involves the transfer of DNA from one bacterium to another with the
use of a bacteriophage (phage).
▪ A phage is a virus that infects bacteria.
▪ The phage T4 and the phage lambda, for example, both infect E. coli.
➢ Phages are obligatory intracellular parasites and must invade a host cell in order to
reproduce.
▪ T4 multiplies by the lytic cycle which kills the host and lamba multiplies by the
lysogenic cycle which does not cause the death of the host cell.
▪ In lysogeny, the phage DNA remains latent in the host until it breaks out in a
lytic cycle.
Types of Transduction
1. Generalized Transduction:
➢ In generalized transduction, any bacterial genes can be transferred because the host's
chromosome is broken down into fragments.
▪ Whatever piece of bacterial DNA available to get packaged within the phage is
the genetic material that will be transferred between cells.
2. Specialized Transduction:
➢ In specialized transduction, on the other hand, only certain bacterial genes can be
transferred.
▪ These genes, as you will see, must exist on either side of the prophage.
▪ Specialized transduction requires a phage that uses the lysogenic cycle for
reproduction.
Steps of General Transduction
➢ A phage attaches to cell wall of bacterium and injects DNA.

➢ The bacterial chromosome is broken down and biosynthesis of phage
DNA and protein occurs.
➢ Sometimes bacterial DNA can be packaged into the virus instead of
phage DNA.
➢ The cell lyses, releasing viruses.
➢ The phage carrying bacterial DNA infects another cell.
➢ Crossing over between donor and recipient DNA can occur producing
a recombinant cell.
Steps of Specialized Transduction
➢ In the lysogenic cycle, phage DNA can exist as a prophage integrated in the
bacterial chromosome.
➢ Occasionally when the prophage exits it can take only adjacent bacterial
genes with it.
➢ The phage DNA directs synthesis of new phages.
➢ The phage particles carry phage DNA and bacterial DNA.
➢ The cell lyses, releasing the phages.
➢ A phage carrying bacterial DNA infects another cell.
➢ The joined phage and bacterial DNA circularize.
➢ Along with the prophage, bacterial DNA integrates with the recipient
chromosome by a cross over event.
▪ This forms a recombinant cell.
Steps of Specialized
Transduction
Phage DNA directs
the synthesis of new phages
Lytic Cycle begins Phage (virus) consist

both phage DNA
and bacterial DNA
Lysogenic Stage
Gene ra l ized t r a n sd uc t on Specla l lze d t r a ns du c t ion
Phage DNA Bacter ial Prophage DNA

DNA £ I 8? )
Phage infects bacter ial cel l. Bacterial cell has prophage integrated between genes A and 8 .
!
! (
< A• >
Host DNAis hydro lyzed into pie<:es, and phage Occasionally, prophage·DNA exits incorrect ly,
DNA and proteins are made. tak ing adjoin ing bacter ia l DNA w ithit .
! !
Occasional ly a bacterial DNA fragment is Phage particles carry bacterialDNA (here,

packaged in a phage capsid. gene A) alo ng with phage DNA.
lL_ Crossing over Q_

CC:f-10 B)
i Transducin9 phages infect new host cel ls, where
recombination (crossing over) can occur.
i
G"(==
A
;""=s-"" - - - - - Recombinant bacter ia - - - - - - -G"('==A
:i'f==8:;_:..,.,
The recomb inants have genotypes (A• S - ) different
from either the donor (A• s •) or recip ient (A - S - ).
Copyright Cl Pearson Education, Inc., publlShlng as Bec'llarnin Cumm

ings.
ROLE OF
MICROORGANI
SM IN SOIL
FERTILITY
AND CROP
PRODUCTION
Rhizosphere and Phyllosphere effects and manipulation of
rhizosphere microflora to sustain plant productivity
➢The rhizosphere is considered the immediate soil zone around the plant
roots influencing microbial associations, proliferations and activities. It
is characterized by overly complex plant roots, plant growth-promoting
rhizobacteria, microflora and fauna interactions.
➢Rhizosphere effect: The enhancement of the growth of a soil
microorganism resulting from physical and chemical alteration of the soil
and the contribution of excretions and organic debris of roots within a
rhizosphere.
Importance
➢Rhizospheres nurture diverse organisms that are useful in
biogeochemical and physical processes that promote soil health and in
return, support and protect plant growth, agriculture production,
human and animal health.
Rhizosphere and Phyllosphere
➢Microbes inhabiting in rhizosphere interact with plants to neutralize toxic compounds,

fix nitrogen, enable plants to resist disease, heat, flooding, drought; deter pathogens
and predators, and promote nutrient use efficiency.
Phyllosphere
➢The phyllosphere is the aerial region of the plant colonized by microbes; its colonists are
often called epiphytes. Fungi, algae, protozoa, and nematodes inhabit the leaf and stem
surfaces, but the most abundant epiphytes are bacteria (averaging 106–107 cells cm−2).
➢The phyllosphere, aerial parts of the plant, represents the largest biological surface area
on Earth covering about 108 km2 globally and each km2 harbors 1016 -1018 microbes.
➢The leaf structures such as stomata, hairs, and veins greatly influence the microbial
colonization and result in disproportionate colonization on leaves.
➢It is reported that up to 107 microbes per cm2 colonize the leaf surface and bacteria are
the predominant organisms with the population of 108 cells per cm2.
Benefits of Phyllosphere microorganism
➢Phyllosphere microorganisms often have a direct positive influence on plants by

enhancing nitrogen fixation, and promoting the growth of plants, the control
of plant pathogens, and the degradation of organic pollutants.
➢Phyllosphere microflora significantly influences the ecological relationship,
adaptation, growth, resistance, and infection of the plant host.
➢The phyllosphere microbiome affects leaf functions and longevity, seed mass,
apical growth, flowering, and fruit development.
➢Beneficial microbes play an important role in increasing yields of the crop,
removing contaminants, and producing novel substances.
➢Phyllopsphere microbial communities produce plant growth factors like IAA and
cytokines that promote nutrient uptake and crop yield.
Rhizosphere vs Phyllosphere
Soil around the root of plant where microbial The surface of leaf inhabited by microbes is called
Definition
activity is high is called rhizosphere phyllosphere
Plant root secrete exudates that contains
Plant leaf secrete exudates that contains mainly
Exudates mainly organic matters including
amino acids, glucose, fructose and sucrose.
carbohydrates, amino acids, vitamins etc
The rhizospheric microbes establish
Microbe The phyllospheric microbes establish interaction
interaction with root by inhabiting in soil
interaction with leaf by inhabiting on surface of leaf.
around root.
Types of
They may be aerobic or anaerobic They are usually aerobic.
microbes
They promote plant growth by carrying out
various biogeochemical transformation in They promote plant growth mainly by producing
Effects on soil and hence increase amount of plant plant growth hormone and protecting against
plants nutrient in soil. They also produce plant pathogens. They usually do not play role is
growth hormone and protect plant against biogeochemical transformation.
pathogens.
Examples Rhizobium, Azotobacter, Clostridium etc Beijerinckia, Pseudomonas, Alterneria etc

Interaction in Rhizosphere
1. Dinitrogen-Fixation Symbiosis
➢Dinitrogen-fixing bacteria can make unavailable N2 available to the plant.
➢Rhizobia and related bacteria form nodules on the roots of plants.
➢This interaction can be mutually beneficial as the plant provides nutrients and
protection for the bacteria and the bacteria provide N for the plant.
➢These bacteria colonize the root surface and interior cells, and intercellular spaces
between the cortex and endodermis and in the xylem cells of grasses.
➢Along with plant-available N, they may provide other plant growth-promoting
compounds also.
2. Mycorrhizal Associations
➢It is the mutualistic symbiosis of Mycorrahizal fungi with plants.
➢These fungi can be found in the rhizosphere of most plants and form associations with all
gymnosperms and more than 83% of dicotyledonous and 79% of monocotyledonous
plants.
2. Mycorrhizal Associations
➢Mycorrhizal fungi can form structures
either on the outside (ectomychorrhizae)
or inside (endomycorrhizae) of plant
roots.
➢Plant exudation patterns may be
altered after colonization by these
fungi, thus affecting the rhizosphere
microbial and macrofaunal
communities.
Significance of mycorrhizal association
➢The fungal hyphae allow the roots to contact a greater volume of soil.
➢Some types of mycorrhizal fungi increase the solubilization of nutrients such as
phosphorus.
➢They assist the plant in increasing nutrient absorption, especially in stressed
environments (e.g., phosphorus- and water-deficient soils), selective ion uptake, and
provide protection from extremes in the environment.
➢The fungi may also protect plant roots from invasion by pathogens.
➢Extra radicle hyphae of endomycorrhizae secrete glomalin, a glycoprotein that
aggregates soil particles, increasing water-stable aggregates and improving soil
structure.
➢This association can increase the survival and growth of a plant, especially in adverse or
low-nutrient environments, and may have potential in the revegetation of disturbed
sites.
3. Plant Growth-Promoting Organisms

➢Plant growth-promoting organisms enhance seed germination and plant growth and are
often specific bacteria or fungi and different mechanisms are responsible for plant
growth promotion.
➢These organisms have been used in biological control programs to protect plants against
plant pathogens, as biofertilizers to fix atmospheric N2, and in phytostimulation, which
directly improves plant growth through the production of plant growth regulators.
➢Some may make nitrogen more available to plants and have the potential to reduce
application of inorganic fertilizers.
➢These organisms may produce plant growth-stimulating compounds such as gibberellic
and indoleacetic acid.
➢The reduction in pathogen load may also be a mechanism of plant growth promotion.
➢Endophytic bacteria may increase plant growth, confer disease resistance, and aid the
plant in withstanding stresses such as drought.
➢Introduction of plant growth-promoting organisms may change the overall composition
of the microbial community, especially in the rhizosphere.
4. Plant Growth inhibiting Microbes (PGIM)
➢Micro-organisms that inhibit plant growth colonize the rhizosphere and can alter
plant development.
➢The rhizosphere harbors pathogens such as fungi and bacteria that attack germinating
seeds and plant roots.
➢Pathogens may produce extracellular enzymes that liquefy cell walls, thereby allowing
degradation of the cell contents.
➢Some pathogens produce toxins that affect the permeability of the cell membrane or
inhibit an enzyme, leading to interruptions in a metabolic pathway.
4. Plant Growth inhibiting Microbes (PGIM)

➢Polysaccharides produced by some pathogens may block vascular tissues and cause
wilting.
➢Excessive production of auxins and cytokinins, resulting from integration of a tumor-
inducing bacterial plasmid into the plant genome, leads to gall formation in the roots.
➢Feeding by plant-parasitic nematodes exposes root cells to destructive enzymes and
toxic metabolites, which ultimately result in decreased water and nutrient uptake in
plants.
➢Deleterious rhizobacteria (DRB) inhibit plant growth without causing obvious disease
symptoms. These organisms are present on the root surface and may occur in the
intercellular spaces of cortical cells. DRB do not parasitize the plant, but survive on
organic compounds released by plant root cells.
➢PGIM detrimental effects on plant growth are due mainly to the production of
metabolites that disturb plant physiological processes, including phytotoxins, plant
growth regulators, volatile substances, or antibiotics.
5. Bioremediation
➢Industrial development and intensification of agriculture in the past several decades have
contributed to environmental contamination, releasing hazardous wastes into
terrestrial ecosystems.
➢The pollutants and hazardous wastes are toxic and carcinogenic nature, and tendency
to bioaccumulate in humans and other organisms, the timely and cost-effective clean-
up of contaminated areas has become a priority.
➢Plant–microbial systems have potential in bioremediation, a process that utilizes the
natural role of plants and microorganisms in transformation, mineralization, and
complexation of organic and inorganic pollutants.
➢Bioremediation may be facilitated by plant root exudates that show high binding
affinities to certain pollutants or by rhizosphere microorganisms that mineralize
contaminants into their nontoxic derivatives.
➢In contrast to conventional soil remediation technologies, bioremediation is less costly,
utilizes relatively simple technology, and is minimally disruptive to the contaminated
site.
5. Bioremediation
The ‘rhizosphere effect’ on bioremediation may occur in three ways.
➢First, it is thought that carbon substrates from roots stimulate increases in xenobiotic
degrader populations and activity.
➢Second, the presence of dense populations of diverse microorganisms in the
rhizosphere may enhance bacterial conjugation, which could result in the evolution of
new pathways of degradation.
➢Third, plants may provide a substrate that increases the production of the enzymes
involved in mineralization of the hazardous compound.
6. Biological Control
➢The rhizosphere is the location for biological control through the use of pathogens,
parasites, or other predators to reduce the population or activity of another
organism.
➢Three major strategies for biological control are classical, inundative, and integrated
management.
➢The classic approach involves the use of natural enemies for release,
dissemination, and self-perpetuation on target pests.
➢The inundative approach is most often used in the rhizosphere and involves the
addition of a virulent strain of a biocontrol agent to suppress pests. In this case, the
biocontrol agent is not self-sustaining and must be applied to the target host every
season.
➢The integrated management approach is a broad strategy that involves management
practices to conserve or enhance native enemies of pests.
➢Biological control can be used in the management of pathogens, nematodes, and
weeds.
➢The reduction in plant pathogens such as Fusarium oxysporum, Gaeumannomyces
graminis, Pythium, and Phytophthora species due to suppressiveness of some soils
is thought to be due to physiochemical and microbial soil factors.
Disease Host Antagonists
Damping-off (Pythium spp.) Beet, Corn Actinoplanes sp., Pseudomonas
Cucumber aureofaciens 63-28, Trichoderma
longibrachiatum CECT 2606
Sheath blight (Rhizoctonia solani) Rice Pseudomonas fluorescens VO61
Root rot (Rhizoctonia solani) Wheat Bacillus sp.
Take-all (Gaeumannomyces graminis var. Wheat Pseudomonas fluorescens Q8r1-96

tritici)
Fusarium wilt (Fusarium spp.) Chickpea, Bacillus subtilis GB03, Paenibacillus sp.
Cucumber, 300, Fusarium spps
Tomato
Root rot (Phytophthora sp.) Raddish, Pepper, Pseudomonas putida WCS417,
Trichoderma harzianum 2413,
Verticillium wilt (Verticillium dahliae) Egg plant, Talaromyces flavus, Pythium oligandrum
Pepper
Factors influencing the activities of soil microorganisms
1. Cultural practices (Tillage)
➢Cultural practices viz. cultivation, crop rotation, application of manures and fertilizers,
liming and gypsum application, pesticide/fungicide and weedicide application have
their effect on soil organism.
➢Ploughing and tillage operations facilitate aeration in soil and exposure of soil to
sunshine and thereby increase the biological activity of organisms, particularly of
bacteria.
➢Crop rotation with legume maintains the favorable microbial population balance,
particularly of N2 fixing bacteria and thereby improve soil fertility.
➢Liming of acid soils increases activity of bacteria and actinomycetes and lowers the
fungal population.
➢Fertilizers and manures applied to the soil for increased crop production, supply food
and nutrition not only to the crops but also to microorganisms in soil and thereby
proliferate the activity of microbes.
1. Cultural practices
➢Foliar or soil application of different chemicals (pesticides, fungicides,
nematicides etc.) in agriculture are either degraded by the soil organisms or are
liable to leave toxic residues in soil which are hazardous to cause profound
reduction in the normal microbial activity in the soil.
2. Soil fertility: The availability of N, P and K required for plants as well as
microbes in soil determines the fertility level of soil. On the other hand soil micro
flora has greater influence on the soil fertility level.
3. Soil moisture: Water (soil moisture) is useful to the microorganisms in two ways
i.e. it serve as source of nutrients and supplies hydrogen / oxygen to the organisms
and it serve as solvent and carrier of other food nutrients to the microorganisms.
➢Microbial activity & population proliferate best in the moisture range of 20% to
60%.
3. Soil moisture
➢Under excess moisture conditions / water logged conditions due to lack of soil aeration
(Oxygen) anaerobic microflora become active and the aerobes get suppressed.
➢While in the absence of adequate moisture in soil, some of microbes die out due to tissue
dehydration and some of them change their forms into resting stages spores or cysts
and tide over adverse conditions.
➢Therefore, optimum soil moisture (range 20 to 60 %) must be there for better population
and activity of microbes in soil.
4. Soil Temperature
➢Temperature is the most important environmental factor influencing the biological,
physical & chemical processes and of microbes, microbial activity and population in soil.
➢Depending upon the temperature range at which microorganisms can grow and function,
are divided into three groups i.e. psychrophiles (growing at low temperature below 10 °C)
Mesophiles (growing well in the temp range of 20 ° C to 45° C) and thermopiles (can
tolerate temperature above 45° C and optimum 45-60°C).
5. Soil air (Aeration)

➢Microbes consume oxygen from soil air and gives out carbon dioxide.
➢Activities of soil microbes is often measured in terms of the amount of oxygen absorbed
or amount of C02 evolved by the organisms in the soil environment.
➢Under high soil moisture level / waterlogged conditions, gaseous exchange is hindered, and
the accumulation of CO2 occurs in soil air which is toxic to microbes.
➢Depending upon oxygen requirements, soil microorganisms are grouped into categories viz
aerobic (require oxygen for like processes), anaerobic (do not require oxygen) and
microaerophilic (requiring low concentration / level of oxygen).
6. Sunlight
➢Direct sunlight is highly injurious to most of the microorganisms except algae.
Therefore upper portion of the surface soil a centimeter or less is usually sterile or
devoid of microorganisms. Effect of sunlight is due to heating and increase in
temperature (More than 45°)
7. Soil PH
➢Soil reaction has a definite influence / effect on quantitative and qualitative
composite on of soil microbes.
➢Most of the soil bacteria, blue-green algae, diatoms and protozoa prefer a
neutral or slightly alkaline reaction between PH 4.5 and 8.0 and fungi grow in
acidic reaction between PH 4.5 and 6.5 while actinomycetes prefer slightly
alkaline soil reactions.
8. Soil Organic Matter:
➢The organic matter in soil being the chief source of energy and food for most of
the soil organisms, it has great influence on the microbial population.
➢Organic matter influence directly or indirectly on the population and activity of
soil microorganisms. It influences the structure and texture of soil and thereby
activity of the microorganisms
9. Nature of Soil
➢The physical, chemical and physico-chemical nature of soil and its nutrient status
influence the microbial population both quantitatively and qualitatively.
➢The soils in good physical condition have better aeration and moisture content
which is essential for optimum microbial activity.
➢Similarly nutrients (macro and micro) and organic constituents of humus are
responsible for absence or presence of certain type of microorganisms and their
activity.
➢For example activity and presence of nitrogen fixing bacteria is greatly influenced
by the availability of molybdenum and absence of available phosphate restricts
the growth of Azotobacter.
10. Microbial associations / interactions

➢Microorganisms interact with each other giving rise to antagonistic or symbiotic
interactions influences the population and activity of soil microbes to a great
extent.
➢The predatory habit of protozoa and some mycobacteria which feed on bacteria
may suppress or eliminate certain bacteria.
➢On the other hand, the activities of some of the microorganisms are beneficial to
each other.
➢For instance organic acids liberated by fungi, increase in oxygen by the activity of
algae, change in soil reaction etc. favors the activity or bacteria and other
organisms in soil.
11. Root exudates

➢ In the soil where plants are growing the root exudates also affects the distribution,
density and activity of soil microorganism.
➢Root exudates and sloughed off material of root surfaces provide an abundant
source of energy and nutrients and thus directly or indirectly influence the
quality as well as quantity of microorganisms in the rhizosphere region.
➢Root exudates contain sugars, organic acids, amino acids, sterols, vitamins and
other growth factors which have the profound effect on soil microbes.
Role of microorganism in formation of soil organic matter
➢The soil organic matter (SOM) is a complex combination of living

organisms, fresh organic residues, actively decomposing material,
and stabilized organic matter (otherwise known as humus).
➢Soil organic matter (SOM) is mainly composed of carbon, hydrogen
and oxygen but also has small amounts of nutrients such as nitrogen,
phosphorous, sulphur, potassium, calcium and magnesium
contained within organic residues.
➢Soil organic matter also exists as four distinct fractions which vary
widely in their in size, composition and turnover times in the soil.
The size, turnover rate and composition of the four-soil organic matter
Fraction Size (μm) Turnover time Composition

& (mm)
Dissolved <45 (μm) (in Minutes to days Soluble root exudates, simple sugars and
organic matter solution) decomposition by-products. It generally
makes up less than 5% of total soil organic matter.
Particulate 53μm–2mm 2-50 years Fresh or decomposing plant and animal matter with
organic matter identifiable cell structure.
Makes up between 2-25% of total soil organic matter.
Humus <53μm Decadal (0s- Older, decayed organic compounds that have resisted
00s decomposition. Can make up
years) more than 50% of total soil organic matter
Resistant <53μm <2mm 00s-000s Relatively inert material such as chemically resistant
organic matter years materials or organic remnants
(for example, charcoal). Can be up to 10% of soil
organic matter
Decomposition of SOM
Process in the
formation of
soil organic
matter
Process in the formation of soil organic matter
1. Decomposition
➢Decomposition is a biological process that includes the physical
breakdown and biochemical transformation of complex organic
molecules of dead material into simpler organic and inorganic
molecules.
Steps in decomposition
1. Fragmentation
➢It is the initial stage of decomposition. Fragmentation means the breakdown of
detritus into smaller pieces by the detritivores e.g. earthworms, millipedes, dung
beetles, fiddler crabs and sea cucumber.
2. Leaching
➢The fragmented particles may contain a lot of water-soluble nutrients which are
inorganic in nature. These nutrients get dissolved in the water and seep into the
soil and get precipitated in the process of leaching.
3. Catabolism
➢Once the complex material is broken down into smaller particles and the inorganic
nutrients are removed, it is time to convert the detritus into simpler inorganic
compounds. This process is carried out by various fungal and bacterial enzymes
by the process of catabolism.
4. Humification
➢It is the process of formation of a dark colored layer of amorphous substance in the soil
called humus. It cannot be decomposed easily as it is highly resistant to action by microbes.
The layer of humus is very rich in nutrients as it provides high fertility to the soil.
➢Humus affects soil properties. As it slowly decomposes, it colours the soil darker; increases
soil aggregation and aggregate stability; increases the CEC (the ability to attract and retain
nutrients); and contributes N, P and other nutrients.
➢Humus formation is a complex two stage process in which organic residues of plant and
animal origin undergo profound transformation.
1. Complete mineralization (CO2, NO2, NO3, NH3, CH4, H2O etc.)
2. The synthesis of organic compounds with the formation of high molecular weight humic
substances of specific nature.
➢ Lignin -------------- broken into Polyphenols, Phenolic acids
➢ Proteins ---------- Polypeptides and Amino acids
➢ Carbohydrates ------------- Simple sugars
➢ High molecular weights humic acids (HAs) and Fulvic acids (FAs )
5. Mineralization
+It is the final step in the process.
Mineralization is the process of the
degradation of the humus to release
inorganic nutrients eg. CO2, NO2, NO3,
NH3, CH4, H2O etc.
+The phosphatase has key roles in the final
conversion of organically bound
phosphorus to inorganic phosphate. E.g.
Bacillus megaterium, B. subtilis,
Serratia spp., Proteus spp., and
Streptomyces spp. and fungi such as
Penicillium spp., Aspergillus spp. and
Steps in the decomposition of SOM.
Rhizopus spp.
PLANT –
MICROBES
ASSOCIATION
Biological interaction( Microbial Association in Soil)
➢ The various types of possible interactions/associations occurring among the

microorganisms in soil can be:
a) Beneficial:
i) mutualism
ii) commensalisms
iii) proto-cooperation
b) Detrimental / harmful:
i) amensalism,
ii) competition
iii) Parasitism
iv) predation
Symbiotic Nitrogen Fixation
Nitrogen fixation:
• It is a process by which nitrogen (N2) in the atmosphere is converted into
ammonia (NH3).
• Atmospheric nitrogen or molecular nitrogen (N2) is relatively inert: it does not
easily react with other chemicals to form new compounds.
• Fixation processes free up the nitrogen atoms from their diatomic form (N2) to
be used in other ways.
• Nitrogen fixation is essential for all forms of life because nitrogen is required to
biosynthesize basic building blocks of plants, animals and other life forms, e.g.,
nucleotides for DNA and RNA and amino acids for proteins.
• Therefore, nitrogen fixation is essential for agriculture and the manufacture of
fertilizer.
Symbiotic Nitrogen Fixation
➢ Rhizobia Bacteria:
• The first Rhizobia were isolated from root nodules by M. Beijerinck, and
shown to have the ability to re-infect their legume hosts, and to fix N2 in
symbiosis.
➢Rhizobium leguminosarum:
• It is a species of gram-negative, aerobic, rod-shaped bacteria that is found in soil
and which causes formation of root nodules on some, but not all, types of field
pea, kidney bean, and clover.
➢Leguminous plants:
• Leguminous plants are included under the family fabaceae or Leguminosae, most
of them have symbiotic nitrogen fixing bacteria, rhizobia in structures called root
nodules
Mechanism of Symbiotic Nitrogen Fixation
• Symbiotic nitrogen fixation occurs in plants that harbor nitrogen-fixing bacteria
within their tissues.
• The best-studied example is the association between legumes and bacteria in
the genus Rhizobium.
• A symbiotic relationship in which both partners benefits is called mutualism. A
mutualistic symbiosis is an association between two organisms from which each
derives benefit.
• It is usually a longer-term relationship, and with symbiotic nitrogen (N2) fixation,
often involves a special structure to house the microbial partner.
• Each N2-fixing symbiotic association involves an N2-fixing prokaryotic organism,
the microsymbiont (e.g., Rhizobium, Klebsiella, Nostoc or Frankia) and a
eukaryotic, usually photosynthetic, host (e.g., leguminous or non-leguminous
plant, water fern or liverwort).
Basic steps in symbiotic nitrogen fixation:
1. Root Nodule Formation
2. Nitrogenase Activity
3. Gene regulation in root nodules
1. Root Nodule Formation:
➢ Rhizobium bacteria stimulate leguminous plants to develop root nodules, which
the bacteria infect and inhabit. The nodules develop in a complex series of
steps:
➢ Rhizobia can infect their hosts and induce root nodule formation using following
mechanisms:
• Root hair penetration and infection thread formation,
• Entry via wounds or sites of lateral root emergence,
• Penetration of root primordia
i. Rhicadhesin protein helps Rhizobia to attach in root hair. Carbohydrate containing Lectins acts as
receptor site in root cell.
ii. Rhizosphere organisms convert tryptophan in the root exudates to Indole Acetic Acid (IAA) which
results in non-specific curling of the root-hairs.
iii. The capsular polysaccharides of rhizobia play a role in inducing “Shepherd’s Crook”, the site of
infection in roots.
iv. Invagination of the root hair takes place due to the production of polygalactouronase by
rhizobia.
v. After this, infection threads are formed, through which rhizobia enter the host.
vi. When the infection thread reaches a cell deep in the cortex, it bursts out and the bacteria are
liberated out in the cytoplasm.
viii. Each bacterium so liberated gets surrounded by a membrane, pinched off from the infection thread.
Mitotic divisions of the host cell results in the development of a nodule.
ix. Bacteria multiply rapidly and surrounded by membranous envelope.
x. Motile rhizobia, enlarges in size and lose their flagella and power of division.This state of bacteria is
known as Bacteroids.
➢ The space between the bacteroids and the membrane gets filled with
leghaemoglobin. Leghaemoglobin helps bacteria in synthesis of ATP and
Nitrogenase activity.
➢ Nitrogen fixation takes place in these nodules and the effective nodules are pink
in color.
➢ Legume –Rhizobium symbiosis is influenced by a variety of factors like host,
bacterial strains, temperature, light, soil pH, phosphorous, etc.
➢ Rhizobial Nod (Nodulation) factors induces the formation of pre-infection
thread structures, but formation of infection thread requires the presence of
bacterial cells. Passing of an infection thread from cell to cell requires local cell
wall degradation.
➢ The modification of cell wall of root cell induces tip growth which
ultimately lead to formation of infection thread.
2. Nitrogenase Activity:
• Biological nitrogen fixation can be represented by the following equation, in which
two moles of ammonia are produced from one mole of nitrogen gas, at the expense
of 16 moles of ATP and a supply of electrons and protons (hydrogen ions):
N2 + 8H+ + 8e- + 16 ATP = 2NH3 + H2 + 16ADP + 16 Pi
• This reaction is performed exclusively by prokaryotes (the bacteria and related
organisms), using an enzyme complex termed Nitrogenase.This enzyme consists of
two proteins – an iron protein(nitrogenase reductase) and a molybdenum-iron
protein (nitrogenase).
• The reactions occur while N2 is bound to the nitrogenase enzyme complex. The Fe
protein is first reduced by electrons donated by ferredoxin. Then the reduced Fe
protein binds ATP and reduces the molybdenum-iron protein, which donates electrons
to N2, producing HN=NH. In two further cycles of this process (each requiring
electrons donated by ferredoxin) HN=NH is reduced to H2N-NH2, and this in turn is
reduced to 2NH3.
2. Nitrogenase Activity:
➢ One of the characteristics of nitrogenase is that the enzyme complex is very
sensitive to oxygen and is deactivated in its presence.
➢ This presents an interesting dilemma for aerobic nitrogen-fixers and particularly
for aerobic nitrogen-fixers that are also photosynthetic since they actually
produce oxygen.
➢ Over time, nitrogen-fixers have evolved different ways to protect their
nitrogenase from oxygen. For example, some cyanobacteria have structures
called heterocysts that provide a low-oxygen environment for the enzyme and
serves as the site where all the nitrogen fixation occurs in these organisms.
➢ Other photosynthetic nitrogen-fixers fix nitrogen only at night when their
photosystems are dormant and are not producing oxygen.
3. Gene regulation in root nodules:
Various genes are involved in regulation process during entire nitrogen fixation mechanisms:
a. nod-genes:
➢ In the initial stage, host specificity becomes evident. This is controlled by nodulation (nod)
gene.
➢ Some of the nod genes induce the host plant to react by producing nodulins
➢ Some node genes are required for root-hair curling and for cell divisions.
b. nif-genes:
➢ The genes that regulate the nitrogen fixation are called nif-genes.
➢ These are found both in symbiotic and free-living system
c. fix-genes:
➢ The symbiotic activation of nif-genes in the Rhizobium is dependent on low oxygen
concentration, which in turn is regulated by another set of genes called fix-genes.
Non- Symbiotic Nitrogen Fixation:
➢ There are several free-living microorganisms which fix nitrogen in soil.
➢ Azotobacter spp. is the main organisms that fixes nitrogen freely.
➢ Other organisms includes Clostridium, Klebsiella, Chloropseudomonas, Rhodospirrilum,
Anabaena etc
➢ Nitrogenase is the key enzyme involved in nitrogen fixation
➢ Themode of action of nitrogenase is same as symbiotic nitrogen fixation.
➢ The difference between symbiotic and non-symbiotic nitrogen fixation is that in this
method there is no formation of root nodules.
➢ The genetic determinants for nitrogen fixation is nif-genes.
➢ The nif-genes which are present in the bacterium function as the controlling agents of
nitrogen fixation.
➢ There is another genes ntr-genes present in the free-living nitrogen-fixing bacterai
which control the genes that allow growth on poor nitrogen sources.
Associative Nitrogen Fixation
➢ In this type of nitrogen fixation microbes are surface- associated on the roots of plants.
➢ Azospirrilum is associated with the roots of grasses and is capable of fixing atmospheric
nitrogen.
➢ Azospirrilum participates in all steps of the nitrogen cycle except nitrification .
➢ It can fix atmospheric nitrogen in pure culture & under microaerophilic condition too.
➢ A clusterof nif-geneshas beenidentified in Azospirillum, which are considered to
homologues to those of Klebsiella pneumoniae.
➢ In some cases there has been root hair deformation due to the association with
bacterium.
➢ The bacterium invade the cortical and vascular tissues of the host, and lead to
enhancement of the number of lateral roots and root hairs which help in increasing
the mineral uptake by plant.
Blue-Green Algae:
➢ The BGA abundantly distributed in the tropics play important roles in
agriculture.
➢ The first and foremost role is nitrogen fixation.
➢ Most of the Nitrogen- fixing BGA are:
Anabaena,Anabaenapsis,Aulosira, Cylindrospermum, Nostoc, Calothrix, Scytonema,
etc.
➢ BGA also add a bulk of organic matter to soil.
➢ It also synthesize vitamins and growth substance ( Vit. B12, auxins and ascorbic
acids.)
➢ Cyanobacteria are able to survive in extreme environments because of unique
adaptation in which the fix nitrogen.
➢ These days mats of BGA are widely used as biofertilizer.
Mechanism of BGA in Nitrogen Fixation:
➢ Cyanobacteria possess unique mechanisms for the protection of nitrogenase, the nitrogen fixing enzyme, against
O 2.
➢ Since diazotrophic cyanobacteria have the ability simultaneously to generate O2 and fix N2, the
mechanisms that N2-fixers use in order to protect nitrogenase from O2 may be particularly well-
developed in cyanobacteria.
1. Heterocystous cyanobacteria:
➢ Heterocystous cyanobacteria are those bacteria which produce sheterocysts.
➢ Heterocysts are specialized nitrogen fixing cells formed during nitrogen starvation by some filamentous
cyanobacteria such as Nostoc, Cylindro spermum, & Anabaena.
➢ Upon nitrogen starvation, some filamentous cyanobacteria start a programme of differentiation that leads
to the formation of heterocysts.
➢ These cells appear at semi-regular intervals along the filaments and are the sites of N2 fixation.
➢ Heterocysts protect nitrogenase from inactivation by O2 by several mechanisms, including a high rate of
respiration and decreased permeability to O2.
Mechanism of BGA in Nitrogen Fixation:
2. Non-heterocystous cyanobacteria:
➢ Typically, they fix N2 in the dark, and photosynthesise in the light. However, it is now
emerging that different non-heterocystous cyanobacteria achieve this in different ways.
➢ In some, Nitrogenase proteins are turned over only when bacteria are fixing nitrogen.
➢ In other, the patterns of nitrogen fixation is endogenous.
Azolla-Anabaena Symbiosis
➢ The association between Azolla & Anabaena azollae is a symbiotic one,
where in the eukaryotic partner Azolla houses the prokaryotic
endosymbiont Anabaena in its leaf cavities & provides carbon sources
and in turn obtains its nitrogen requirements.
➢ This mutual exchange of activities helps in quick growth and
multiplication of the fern under optimal environmental conditions.
➢ This symbiosis helps to grow successfully in habitats lacking or having low
levels of nitrogen under waterlogged conditions.
➢ Mutually, they grow together at the surface of quiet streams and ponds
throughout tropical and temperate region of the world.
➢ Under microscopic examination, every Azolla sample will have filaments
of Anabaena living within ovoid cavities inside the leaves.
Significance of Azolla-Anabaena Symbiosis
➢ Useful in rice paddies farming.

➢ Capacities of fixing nitrogen become cheaper and faster
➢ Help in enrichment and maintaining soil fertility
➢ Offers sound ecological sustainability on a long-term basis
➢ Can be uses as green manure, water purifier, animal feed etc
Mycorrhiza
➢ The symbiotic association of fungi with roots of higher plants is known as
mycorrhiza,
➢ In a mycorrhizal association, the fungus colonizes the host plant's roots,
either intracellularly as in arbuscular mycorrhizal fungi (AMF or AM), or
extracellularly as in ectomycorrhizal fungi.
➢ The structure and development of mycorrhizal fungus hyphae is substantially
altered in the presence of roots of host plants. These root- borne hyphae
are distinct from hyphae which are specialised for growth in soil.
➢ All mycorrhizas have intimate contact between hyphae and plant cells in an
interface where nutrient exchange occurs.
➢ The primary role of mycorrhizas is the transfer of mineral nutrients from
fungus to plant. In most cases there also is substantial transfer of metabolites
from the plant to fungus.
Types of Mycorrhiza
There are four main types of mycorrhizae:
1. Ectomycorrhiza:
➢ In ectomycorrhiza , the fungus forms a compact mantle or sheath over the root
surface and the hyphae grow out into the soil.
➢ They are mostly found in the forest tress.
➢ Basidiomycetes fungi producing mushroom (e.g. Amanita, Boletus) or puffball
(Rhizopogon, Pisolithus) type fruiting bodies are the common fungal symbionts.
➢ The mycorrhizal hyphae assume at least partly the functions of root hairs.
➢ Radioactive- labelling studies have shown that nitrogen, P, Ca, applied to soil can
enter the plants through mycorrhiza.
➢ The ectomycorrhizal fungi help in the phosphorous nutrition of plants through
increased surface area of absorption, offer protection against some plant
pathogens, and enhance rooting and survival of cutting through production of
growth hormones.
Types of Mycorrhiza
2.Vesicular arbuscular (VA) mycorrhiza:
➢ TheVA mycorrhiza have a loose network of hyphae in soil and an extensive growth within the
cortex of the plant.
➢ In the host cells they produce highly branched hyphal structures, called arbuscules and also
vesicles.
➢ They are found in a wide variety of host plants, including most of the crop plants.
➢ The fungi involved are Glomus,Acaulospora, Sclerocystis,Entrophospora etc.
➢ These mycorriza improve plant growth through better uptake of P & Zn from soil.
➢ It also penetrates the outermost cortex region, when the plant is well supplied with
Phosphorous, but in phosphorous- deficient plants they penetrate deep into cortex and help
plant to obtain nutrient from the soil.
➢ It also stimulate beneficial organisms like Rhizobium,Azotobacter, and phosphate solubilizers in
the rhizossphere and suppress the growth of root pathogenic fungi and nematodes.
Fig: VAM
Types of Mycorrhiza
3. Ericoid Mycorriza:
➢ Ericoid mycorrhizas are the third of the three more ecologically important types.
➢ They have a simple intraradical (grow in cells) phase, consisting of dense coils of hyphae in
the outermost layer of root cells.
➢ It is seen mostly in the family like blueberry and Erica plants.
➢ Pezizella ericae, an ascomycetes is most common fungal symbiont.
➢ Ericoid mycorrhizas have also been shown to have considerable saprotrophic capabilities,
which would enable plants to receive nutrients from not-yet-decomposed materials via the
decomposing actions of their ericoid partners.
4. Orchidaceous Mycorrhiza:
➢ All orchids are infected at some stage in their life cycle by the orchidaceous mycorrhizal fungi.
➢ After establishment of a mycorrhiza, organic carbon and other nutrients are passed from the
fungus to the orchid seed.

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Agricultural

•Microbiology is the study of living organisms of microscopic

• Their size is very small.

• There is no cellular differentiation.

• Microorganisms are present everywhere on the bodies

E.Discovering the effect of microbes on organic and inorganic

include Ruminococcus and Clostridium.

• Involved in nutrient transformation process

Pro = before (primitive)

➢Flagella (singular – flagellum)

➢Prokaryotes continue to have an enormous ecological impact.

➢Prokaryotes, along with fungi, are decomposers that recycle chemical

➢Some prokaryotes live with other species in symbiotic relationships.

➢Some parasitic prokaryotes are pathogenic, causing disease in the host.

➢Bacteria have been put to work in laboratories, sewage treatment

Pro = before (primitive)

• Prokaryotes are the single-celled organisms and much smaller than

5. Genetic Material of Prokaryotes:

➢Prokaryotes continue to have an enormous ecological impact.

➢Prokaryotes, along with fungi, are decomposers that recycle chemical

➢Some prokaryotes live with other species in symbiotic relationships.

➢Some parasitic prokaryotes are pathogenic, causing disease in the host.

➢Bacteria have been put to work in laboratories, sewage treatment

➢ The time in which population of microorganism doubles.

➢ Bacteria reproduce by the process of binary fission.

➢ Transverse binary fission

➢ Genetic transfer is the mechanism by which DNA is transferred from a donor to a

➢ Bacterial transformation has been demonstrated in several bacteria. For

➢ A second mechanism by which genetic transfer takes place is conjugation.

Therefore, we will briefly review plamid structure before continuing.

➢ A phage attaches to cell wall of bacterium and injects DNA.

Lytic Cycle begins Phage (virus) consist

Phage DNA Bacter ial Prophage DNA

Occasional ly a bacterial DNA fragment is Phage particles carry bacterialDNA (here,

lL_ Crossing over Q_

Copyright Cl Pearson Education, Inc., publlShlng as Bec'llarnin Cumm

➢Microbes inhabiting in rhizosphere interact with plants to neutralize toxic compounds,

➢Phyllosphere microorganisms often have a direct positive influence on plants by

Examples Rhizobium, Azotobacter, Clostridium etc Beijerinckia, Pseudomonas, Alterneria etc

3. Plant Growth-Promoting Organisms

4. Plant Growth inhibiting Microbes (PGIM)

Root rot (Rhizoctonia solani) Wheat Bacillus sp.

Take-all (Gaeumannomyces graminis var. Wheat Pseudomonas fluorescens Q8r1-96

5. Soil air (Aeration)

10. Microbial associations / interactions

11. Root exudates

➢The soil organic matter (SOM) is a complex combination of living

Fraction Size (μm) Turnover time Composition

➢ The various types of possible interactions/associations occurring among the

➢ Useful in rice paddies farming.

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