Ph.D Programs in Agricultural Microbiology

Academic program in Agricultural Microbiology
Ph.D., Program
Course
Code
Course Title
Credit
hours
Major (15 Credits)
AGM 601* Advances in Fermentation 2+1
AGM 602* Advanced Microbial Physiology 2+0
AGM 603* Regulation of Microbial Biosynthesis 2+0
AGM 604* Current Topics in Soil Microbiology 2+0
AGM 605 Microbial Gene Technology 2+1
AGM 609 Plant - Microbe Interactions 3+0
Minor (8 Credits)
AGM 606 Immunology & Serology 2+1
AGM 607 Metabolic Diversity in Microorganisms 1+1
AGM 608 Advanced Methods for Identification of Microorganisms 2+1
ENS 612 Environmental biotechnology and Nanotechnology 1+1
MBB 603 Advances in Microbial Biotechnology 3+0
SAC 605 Biochemistry of Soil Organic matter 2+0
Supporting Courses (5 Credits)
MAT 604* Modeling for agricultural sciences 1+1
ENS 616 Anaerobic systems and Biogas production 1+1
SAC 602 Advances in Soil fertility 2+0

MBB 602 Advances in Genetic Engineering 3+0
PFE 602 Advances in Food Processing 3+0
Seminar and Research
AGM 691 Seminar I 0+1
AGM 692 Seminar II 0+1
AGM 699 Research 0+45
* Compulsory courses
1. MAJOR COURSES 
1.1.AG - Advances M 601 in Fermentation (2+1)
Objective
industrially useful microorganisms
To teach students reg
including yeast technology.
Unit I
An -current overview status offerm fermentation entation industry.
Fermentor designs, high performance bioreactors. Methods of
fermentations, Fermentation kinetics- mass and energy transfer in
bioreactors. Instrumentaion and control in fermentors-online
measurements systems, Biosensors, computer application.
Unit II
Media for microbial fermentation: criteria in media formulation. An
overview of downstream processing.
M icrobiology ofIn
Unit III
Screening for new m
industrially important microbes and their genetic manipulations.Products
from fermentation industries. Microbial production of health care products.
Biocatalysts and bioprocessing. Antibiotic fermentation research: Microbial
transformations- steroid transformation-Microbial colourants.
Unit IV
metabolites. Treatment of biological wastes, microbial inoculants and
enzymes for waste treatment-Value addition through microbial
Recentdevelopm e

fermentation.
Unit V
Yeasttechnology
-classification, genetics, selection and strain
improvement for brewing and distilleries. Response surface methodology
(RSM)-concept and its applications - Scale up of fermentations.
Practical
Industria ly im po
Fermentation by improved strains of yeast for production of alcohol and
beer, Industrial visit of alcohol, beer and cheese production units,
Microbial production of important antibiotics, enzymes and organic acids,
Probiotics, Pigment(Organic colourant) production, Isolation of anaerobes,
Bioremediation of industrial effluents
Lecture schedule
1. Importance of fermentation and its historical perspectives. 2. Current
status of fermentation industries
design and its application
3.M ethodsof
5. High performance bioreactors 
6.Ferm entation k
energy transfer in bioreactor
8. Different types of instrumentation 
9.Com control m on m easure
systems
10.O -biosensors-computer
nline m easurem entsystem s
application
11.M icrobiology
processes-Inoculum preservation, growth and production 
13.
Fermentation processes-substrates (media)
14.Downstream
processingoverview
15.Downstream -unit operations in processing product
recovery
16.Screening fo
New strategies for isolation of industrially important microbes-genetic
manipulations 19. Overview on products from microbial fermentation 
20.
Microbial production of healthcare products
21.Antibiotic
fermentation
22.M -types,procedures icrobialtransform and ations
applications
23.Steroid transform
Recent developments on production of primary and secondary
metabolites.
26.O verview on the
Treatment of biological wastes using microbial inoculants and enzymes 
28.

Treatment of biological wastes using microbial inoculants and enzymes 
29.
Value addition through microbial fermentation
30.Yeasttechnology
-
classification and genetics
31.Selection and str
brewing, baking and distilleries
32.Application and im p
biocatalysts in microbial industries
ogyconcept
33.Response surface
and its applications.
34.Scale up offerm
en
Practical schedule
1. Isolation and screening of industrially important microbes from different
samples 2. Isolation and screening of industrially important microbes from
different samples 3. Culture improvement by physical mutation 
4.Culture
improvement by chemical mutation
5. Testing of improved strains for maximum efficiency 
6.W ork exper
on fermentor designs and their different parts- running a lab scale
fermentor
7.Production
of alcohol and beer- Industrial visit to have a
practical exposure on large scale
production under continuous fermentation.
8.Production o
lab scale fermentor and testing the efficiency
9.Production ofc
enzyme by solid state fermentation and testing the efficiency 10.
Production of organic acid(Acetic acid)
11.Production ofprob
microbes
12.Pigm ent(O
enzyme activity from commercially available samples
14.Isolation and
enumeration of anaerobes-roll tube technique.
15.Biorem ediation o
industrial effluents-reed bed method
16.Decolourisation
effluent by microbes
17.Practicalexam ination.
2
Suggested readings
Cruger,W and A.Cruger.2004.Biotechnology-A Textbook of Industrial
Microbiology.2 nd Ed. Panima Press, USA. 
EL -Mansi, E.M.Y and
C.F.A.Bryce.2004. Fermentation Microbiology and Biotechnology. Taylor
and Francis, London.

Peppler.H.J and D.Perlman.1979.Microbial Technology.2 nd Ed.Academic
Press, NY. 
Reed.G Prescott .1987. and Dunn’s Industrial Microbiology.4 th
Ed.CBS, NY
Stanbury .P.F and A.W h
Fermentation Technology. Pergamon Press, NY.
1.2. AGM 602 Advanced Microbial Physiology (2 + 0)
Unit I
various cell components.
Unit II
Unit III
shock proteins.
Unit IV
molecular 
O rigin,evolution,structure,function aspects of
and
Differentiation in bacteria,slim e
M olecular biology
Extrace - cell signaling. luar proteins secretion in b
Unit V
M - Analysis etabolic of flux metabolic analysis balance -
Extremophiles – mechanisms of adaptation to various ecological
conditions.
Lecture schedule
1. Molecular logic of life – prebiotic evolution
2. Chemical unity of diverse living organisms
3. Evolutionary relationship among microorganisms – evolution and
structure of prokaryotic cells.
4. Evolution of eukaryotic cells – major structural features of eukaryotic
cells
5. Evolution of multicellular organisms and cellular differentiation
6. Microbial phylogeny – Phylogenic tree
7. Chemical composition and macromolecular constituents of gram positive

acteria
8. Chemical composition and macromolecular constituents of gram
negative bacteria
9. Chemical composition and macromolecular constituents of slime molds
10. Chemical composition and macromolecular constituents of yeasts
11. Functions of various cell organelles
12. Structural hierarchy
13. Supra molecular architecture of membranes
14. Solutes transport across membranes
15. Bioenergetics – energy balances in microbial metabolism
16. Biological oxidation and reduction reactions
17. Mid semester examination
18. Bioluminescence – principles and mechanism
19. Molecular aspects of bioluminescence
20. Bacterial virulence -vir proteins
3
21. Biological effects of various vir proteins in bacterial pathogens
22. Heat shock proteins – principles and mechanism of protein
secretion
23. Regulation of heat shock proteins

24. Molecular basis of cell – cell signalling – protein secretion
25. Receptor enzymes and second messengers – cytokines and steroid
receptors
26. Signal transduction of a cell death signal- Apoptosis
27. Essential signals in the environment and host response
28. Quorum and antiquorum sensing in proteobacteria
29. Emergent properties of quorum sensing
30. Bacterial toxins – toxins acting on cell surfaces – toxins with
intracellular target
31. Production of antimicrobial compounds – mechanisms of action
32. Metabolic flux analysis
33. Types of Extremophiles – barophiles, halophiles etc.,
34. Mechanisms of adaptation to various extreme environments.
Suggested readings
Nelson, D.L. and M.M.Cox. 2005. Principles of Biochemistry. Fourth
edition, MacMillan Press Ld., UK
Weaver, R.W. 2000. Molecular Biology. Mcgraw – Hill Publications, New
York 
Dun ny, G.M. and S.C.Winans. 2000. Cell –cell signaling, ASM Press,
Washington. 
C ossart,P .,P .
Cellular Microbiology. ASM Press, USA.
1.3. AGM 603 - Regulation of Microbial Biosynthesis (2 + 0)
Objective
Course ts thorough im par knowledge about the synthesis of
biomolecules in microorganisms by various pathways and their regulation.

Unit I
Regulation -termination ofinitiation,term ination and
transcription.
G lobalregulation and d
Regulatory controls in bacteria - inducible and biosynthetic pathways.
Unit II
Ribosom alRNA an
condition. Specific regulatory systems; SOS regulatory control; Antisense
RNA regulation of gene expression.
Unit III
pathways. Regulation of cell cycle. Lytic and lysogenic cascade.
Unit IV
recent topics of regulatory systems of current interest.
O xidative stress
G lobalnitroge
4
Lecture schedule
1. Regulation of initiation and termination of transcription in inducible
pathways of macromolecules in bacteria
2. Regulation of anti-termination of transcription in biosynthetic pathways
of macromolecules in bacteria
3. Global regulation and differentiation by sigma factor
4. Specific regulatory systems and SOS regulatory control
5. Regulatory controls of inducible and biosynthetic pathways
6. Anti-sense RNA regulation of gene expression
7. Regulation of amino acids synthesis
8. Regulation of protein synthesis
9. Regulation of fatty acids synthesis

10. Regulation of lipid synthesis
11. Regulation of glycoproteins and lipoproteins and glycolipids
biosynthesis
12. Regulation of glycoproteins and lipoproteins and glycolipids
biosynthesis
13. Synthesis and regulation of proteins under stress conditions
14. Synthesis and regulation of lipids under stress conditions
15. Synthesis and regulation of complex polymers under stress
conditions
16. Synthesis and regulation of complex polymers under stress
conditions
17. Mid Semester examination
18. Oxidative stress control
19. Fermentative regulatory pathways in the synthesis of secondary
metabolites
20. Regulation of respiratory pathways in the energy production
21. Regulation of cell division in bacteria
22. Regulation of cell division in fungi
23. Regulation of lytic and lysogenic cascade in phage bacteria
interactions
24. Global control of biosynthetic pathways
25. Regulation mechanisms in the biosynthesis of surfactants

26. Regulation mechanisms in the biosynthesis of growth regulators
27. Regulation of nitrogen fixation
28. Gene control of quorum sensing
29. Regulation of biosynthetic pathways in extremophiles - thermophiles
30. Regulation of biosynthetic pathways in extremophiles - halophiles
31. Regulation of biosynthetic pathways in extremophiles – barophiles
32. Regulation of biosynthetic pathways in bacteria capable of
degrading recalcitrant 
substances
33. Regulation of chromosomal repair mechanisms in bacteria
34. Summing up and review
Suggested readings
Lewin, B.. 2003. Gene VIII. Pearson Education, NY. 
Ingram ,V.M .196
The Biosynthesis of Macromolecules. Benjamin Inc, New York.
1.4. AGM 604 - Current Topics in Soil Microbiology (2 + 0)
Objective
diversity, biological control and bioremediation
To m ake stud
5
Unit I
and dispersal of microorganisms.
Unit II
microorganisms in soil fertility.
M olecular ecolo
M icrobialsucc
Unit III
Biorem of polluted ediation soils; Biological control

Unit IV
O ther topics ofcurrentinterest
Lecture schedule
1. The soil habitat – microhabitats in soil – heterogeneity of microhabitats
2. Manipulation of physiochemical and biological factors in soil
3. Soil microbial community – use of genetic markers to investigate
community structure and
diversity ofm icroorganism s
4. Molecular tool box for ecological studies in soil – DNA extraction
techniques
5. Diversity of microbial 16S r DNA in soils- methodological problems of
16S r DNA based studies.
6. Gene stability and assessment of gene transfer in the phytosphere.
7 Microbial biomarkers – cell envelope markers-biochemical markersnucleic
acid biomarkers
8. Microbial population as biomarkers.
9. Physiological and metabolic aspects of the survival of bacteria
introduced into the soil
10. Bacterial colonization of the rhizosphere and plant roots
11. Bacterial colonization of soil and adaptation to soil conditions
12. Soil and rhizosphere conditions affecting introduced bacteria
13. Survival, dispersal and persistence of genetically modified
microorganisms (GMM) after field 
release
14. Microbial processes within the soil – soil heterogeneity – physical,
chemical and biological
heterogeneity.

15. Microbial activity in soil and factors influencing their growth and
survival.
16. Population activity of specific organisms
17. Mid Semester Examination
18. Measurement of specific processes – carbon transformation –
transformation of organic matter
19. Cellulose, hemicelluloses degradation
20. Lignin degradation
21. Role of microorganisms in soil fertility
22. Nitrogen transformation – nitrogen fixation
23. Phosphorus and other mineral solubilization
24. Microbial inoculants – importance in soil nutrient cycling and soil
fertility
25 Bacterial inoculants 
26.Fungaland
biological disease control
28 Com m ercia ly succe
agents
29.Production and applica
Bioremediation of polluted soil – important pollutants and their sources 
3 1.
Xenobiotics – microbial attack on xenobiotic materials - Microbial
degradation of pesticides
32.Biodegradation
chlorophenols in soil -aerobic and anaerobic
degradation
6
33. Heavy metal toxicity – bioremediation of heavy metals
34. Role of
mycorrhiza in bioremediation of heavy metals in polluted soil

Suggested readings
Annable, M.O., M. Teodoresen, P. Hlavinek, and L. Diels. 2008. Methods
and Techniques for cleaning up contaminated sites. Springer-Verlag, New
York.
Bardgett,R.D
. 2005. The Biology of soil: A community and
ecosystem. Oxford Univ. Press Inc., New York.
Copping, L.G. 2009. The manual of biocontrol agents. Fourth Edition.
British Crop Protection Council Series, UK.
Helyer,N.,K.Brown
N.D.Cattlin. 2009. Biological Control in plant protection. Manson Publ.,
London, p.128.
Paul, E.A. 2007. Soil Microbiology, Ecology and Biochemistry. Third
Edition. Elseiver Pub., Amsterdam.p. 514.
Applied bioremediation and phytoremediation. Springer-Verlag, New York.
p.281.
Singh,A.and
Subba Rao, N.S . 2008. Soil Microbiology. Fourth Edition. Oxford and IBH
Pub., New Delhi.
Tate,R.L.200
Wiley & Sons Inc., New York. P.398. vanElsas, J.D, J.K.Tansson and
J.T.Trevors. 2006. Modern Soil Microbiology. Second Edition. CRC Press,
New York. p. 672.
Verm a,A.and R.O elm u
Techniques in Soil Microbiology. Springer, NY. p. 427.
1.5. AGM 605 Microbial Gene Technology (2+1)
Objective
recombinant DNA technology.
To e with m ake microbial students genomes fam iliariz for use in
Unit I
M - genetic olecular elements concepts – in m icrobialgenetics
Molecular aspects of gene expression – genotypic and phenotypic
variation – regulation of gene expression – ‘Lac’ operon and operon
models.
- 
Developm tools and techniques-
entofm icrobialm olecular b
Unit II
extra chromosomal and
chromosomal DNAs - Analysis of DNA-Electrophoresis - DNA

manipulative enzymes - Polymerase Chain Reaction (PCR) - different
versions of PCR- application of PCR methods
Unit III
Cloning - vectors based on p
construction of recombinant DNA molecules-Introduction of recombinant
DNA into bacterial cells- Transformation, transduction, conjugation,
electroporation.
Unit IV 
Const ruction of genomic library and cDNA library - Identification of
correct clone through primers, probes & antibodies - DNA sequencing –
Methods in Genome sequencing - expression of cloned genes in
homologous & heterologous hosts – 16S rRNA, molecular markers, GFP,
lacZ, GUS.
Expression in recipient cell – methods of scoring markers – DNA
hybridization, southern blotting, western – western blot techniques –
screening for DNA polymorphism – RAPD- VNTRs- SSRs- Gene tagging
and techniques for DNA finger printing.
7
– 
UnitV
Application in m
Practical
Isolation - ofbacterialgenom plasmid DNA ic DNA
from bacteria - Agarose gel electrophoresis of DNA - Restriction digestion
of DNA-Restriction mapping - Ligation of DNA molecules - Microbial DNA
amplification by PCR, random primers, specific primers - Transformation
of E.coli-screening of transformants - expression of cloned genes in E.coliplasmid
curing in beneficial microbes-bacterial conjugation- transposon
mutagenesis- lysogenic and lytic phage- phage DNA isolation.
Lecture Schedule
1. Microbial genetics - Genetic elements in microbes
2. Tools & techniques for molecular biology
3. Genetic and phenotypic variation
4. Molecular aspects of gene expression

5. lac operon and other operon models, fine structure
6. Types of plasmids and plasmid controlled characters
7. Conjugation and fertility factor in bacteria
8. Transposons mutagenesis
9. Bacterial transformation - theory and concept
10. Mapping of genes by transformation
11. Transduction - Generalized and specialized transduction
12. Mutation in microorganisms – spontaneous and induced
13. Mutagens – mechanism, mutation frequency & and reversion
14. Preparation of DNA from microbial cells
15. DNA manipulative enzymes
16. Plasmids as cloning vectors for E. coli
17. Mid semester examination
18. Bacteriophages as cloning vectors for E. coli
19. Cloning vectors for other microbes
20. Polymerase Chain Reaction
21. Construction of genomic library and cDNA Library
22. Direct and indirect selection of clones
23. DNA analysis for clone identification

24. Protein analysis for clone identification
25. Studies on the cloned genes
26. Genome structure and genome sequencing
27. DNA sequence analysis- Chemical and enzymatic methods
28. Methods of scoring markers.
29. DNA hybridization techniques – southern, northern and western blot.
30. Screening for polymorphism – RFLP, AFLP, UNTRS etc.,
31. Gene expression vectors
32. Production of recombinant proteins in E.coli
33. Production of recombinant proteins in eukaryotic cells
34. Problems with the production of recombinant proteins
Practical schedule
1. Isolation of bacterial genomic DNA
2. Isolation of plasmid DNA from E. coli
3. Agarose gel electrophoresis of DNA
4. Plasmid curing in bacteria
5. Conjugation in bacteria
8
6. Induction of mutation in microbes by Chemical agents

7. Induction of mutation in microbes by physical agents
8. Restriction digestion of plasmid and genomic DNA
9. Size determination of DNA molecules
10. Restriction mapping
11. Elution of DNA from Agarose gel
12. Ligation of DNA molecules
13. Preparation of E.coli competent cells
14. Transformation of E.coli -lacZ selection of recombinant E.coli
15. Expression of cloned gene in E. coli (SDS-PAGE of proteins)
16. Microbial DNA amplification by PCR
17. Practical examination
Suggested readings
Ausubel. F.M., R.Brent, R.E.Kingston, D.D.Moore, J.G.Seidman,
J.A.Smith and K. Struhl. 1999. Short Protocols in Molecular Biology.
Fourth Edition. John Wiley & Sons, Inc. New York.
Gene Cloning and DNA Analysis: An Introduction. Fourth Edition.
Blackwell Science Inc., Oxford, UK.
Brown.T.A.2001.
Primrose. S., R. Twyman and B. Old. 2001. Principles of Gene
Manipulation. Sixth Edition. Blackwell Science Limited, Oxford.
J., E.F. Fritsch and T. Maniatis. 2000. Molecular Cloning: A laboratory
Manuel. Hird Edition. Cold Spring Harbor Press, New York.
Sam brook,
Streips, U.N. and R.E. Yasbin. 2006. Modern Microbial Genetics. Wiley –
Liss. John Wiley & sons, Inc. Publication, NY.

Outcome
gene technology.
Students wila
1.6. AGM 509 Plant - Microbe Interactions (3+0)
Objectives
9
•To familiarize the students with the biochemical and
biophysical mechanisms, genetics, genomics, proteomics and
advanced microscopy, spectroscopy of different interfaces of
beneficial and pathogenic plant microbe interactions.
•Molecular analysis of relevant factors in the plant and
microbes, and components that modulate plant-microbe interactions
for soil and plant health for sustaining crop productivity. 
 Unit
I
Nature ofm icro
interfaces of interactions - Plant- microbe, soil microbe, soil-plantmicrobe
interactions leading to symbiotic (rhizobial and mycorrhizal),
associative, endophytic and pathogenic interactions. Types of
ecosystems: Concept and dynamics of ecosystem, Food chain and
energy flow, Microbial communities in the soil. Microbial colonization
in plant roots, Plant root border cells production of cell specific
chemo attractants, nod gene inducers, phytoalexins and
phosphatases. 
 Unit II 
Q -sensing uorumin bacteria, flow of signals
in response to different carbon or other substrates and how signals
are recognized. Molecular basis of rhizosphere colonization. Signal
molecules for plant
microbe interactions, their genes involved in various responses to signal
molecules Community dynamics and population interactions employing
DGGE, TGGE, T-RFLP.
Unit III
M -microbe ethodology/resources interaction, to study plant
recombinant inbred lines, biosensors Decomposition of organic matter in
soil. Antagonism among soil microorganisms, Transcriptome profiling,

metabolic profiling, genomics, proteomics and advanced microscopy,
spectroscopy of different interfaces.
Unit IV
Plantand m icro
and specific regulators for different interactions. Interactions of plant root
symbionts and pathogens; types of interactions - N2 fixing microorganisms
and their interaction- Mycorrhizal relationships - metabolic function of VAM
fungi – and ecto and other mycorrhizal fungi. Molecular diversity of
microbes, plants and their interactions including transgenic microbes and
plants.
Lecture schedule
1. Nature of microbial interaction in soil ecosystem
2. Microbial interaction with plant - beneficial and harmful relations
3. Interaction in soil-plant microbes - symbiotic and asymbiotic relation
4. Role of microbes in endo-symbiosis and mycorrhizal colonization
5. Pathogenic interaction among living entities
6. Associative symbiotic relation and its significance in soil
7. Concept of ecosystems and its types of ecosystem ,components and
variablities
8. Community and ecosystem dynamics
9. Food chain and energy flow
10. Energetic of microbial growth: concept of energy flow in soil
11. Role of microbes in nutrient transformation in soil ecosystems 
Role
of microbes in organic matter degradation - kinetics and
mathematical model of 
decay

13. Association of microbial communities
14. Community dynamics and its interaction employing DGGE
15. Community dynamics and its interaction employing TGGE
16. Community dynamics and its interaction employing T-RFLP
Quorum sensing in bacteria-[Signal transduction · Apoptosis ·
Second messenger system 2+ 
Ca signaling, Lipid signaling] and
agents for quorum sensing
18. Flow of signal pathway [MAPK/ERK pathway · Notch signaling
pathway · JAK-STAT
signaling pathway · cA
pathway · Akt/PKB signaling pathway
19. Plant root border cell production
20. Bacterial repellent; molecular basis of rhizosphere colonization
Signal molecules for plant microbes interaction, their generation
perception and
transduction
22. Genes involved in response to signal molecules, nif, nod and sym
genes
23. Role of enzymes and cofactor stimulating root colonization
24. Flavonoids and isoflavonoids in root colonization
25. PGPR in the rhizosphere helper bacteria and their interactions
26. Mid Semester Examination
27. Association of microbes in rhizosphere, philosphere and
spermosphere regions
28. Siderophore production and their role in plant defense mechanism

12.
17.
21.
10
29. Intercellular colonization of VAM
30. Metabolic function of VAM and their interaction in plants
31. Metabolic function of VAM: carbohydrate and mineral nutrients
32. Association of recombinant inbred lines and their interaction
33. Biosensors and biochips as a biosensing elements on toxicity
34. Transcriptome profiling to assess genes in rhizosphere interactions
35. Community genomics in microbial ecology and evolution
assessment
36. Proteomics as a tool to plant microbial interaction
37. Application of advanced types of microscopy techniques for
microbial interaction
assessm ent
38. Spectroscopy utilization for ascertaining the plant microbes
interaction
39. Identification of antimicrobial effect among plant and microbes
40. Microbial and microbial gene interaction and signal exchange
41. Global and specific regulation mechanism of microbial interaction in
molecular genetics
and biotech approaches

42. Molecular diversity of microbes
43. Physiology of VAM on transport of nutrition
44. Associative and symbiotic relation and its significance
45. Role of archea association in extreme environments
46. Endophytic associations and its significance
47. Assessing the antagonistic activities among soil microbes
48. Microbial associations in anaerobic environments
49. Transgenic plant – microbe interaction
50. transgenic microbes - rhizoremediation process
51. Review of classes
Suggested readings
Biswas, B.B. and H. K. Das 1998. Plant- Microbe Interactions. Kluwer
Academic Publishers, NY Stacey, G. and N.T.Keen 1995. Plant-Microbe
Interactions. Kluwer Academic Publishers, NY Boland, G. and L. Bolis,
1998 Plant-microbe Interactions and Biological Control CRC Press.USA
Stacey, Keen, N. and G.S. Stacey 1997 Plant-Microbe Interactions ISBN:
9780412112416 : Springer USA, p.240.
2. MINOR COURSES 
2.1.AG - IMMUNOLOGY M 606 AND SEROLOGY
(2+1) Objective
To understand basic principles and applications of immunology To
develop practical skills in serology
Unit I
G – Historical eneralPrinciples background ofIm – mcurrent
unology
problems in Immunology – Infections and Diseases – Bacterial and

viruses –Multiplication and diseases - Key biochemical processes.
Unit II
Antigen – Destruction and of antigenecity foreign materials –
cellular interactions. Antibody structure and function – The lymphoid
organs and lymphocytes - Nature of antibodies. Antigen - antibody
interactions.
11
Unit III
- 
The Immunoglobulin genetic basis - types ofantigen recognition
and distribution IgG synthesis - Molecular biology and functional diversity -
Antigenic determinants - Isotypes, allotypes and idiotypes.
Unit IV
M - Antigen onoclonalantibodies.Cytokines
recognition - Acute
inflammatory response - Antibody response - cell mediated immunity -
lymphocyte activation - regulation of immune response – Transplantation.
Unit V 
Vaccination
- Immunodeficiency - Hypersensitivity - Inflammation
and Allergies - Autoimmunity – The phylogeny of immune systems -
Immunotechnology.
Practical
Serologicaltests
- Electron microscopy. Preparation of antigen -
methods of bleeding - preparation of serum and complement, antigen -
antibody reactions, precipitation test - Immunodiffusion – Immuno
electrophoresis –Complement fixation – affinity chromatography, Western
blot and complementation test - ELISA.
Lecture Schedule
1. General Principles of Immunology
2. Historical background – current problems in Immunology
3. Infections and Diseases – Bacterial and viruses
4. Multiplication and diseases - Key biochemical processes
5. Antigen and antigenecity

6. Destruction of foreign materials – The Myeloid systems- Neutrophils,
Eosinophils, Basophils
and Platelets
7. Cellular interactions – Cell surface proteins, cell surface receptors and
signal transductions
8. Antibody structure and function
9. The lymphoid organs and lymphocytes – Source of lymphoid organs – T
and B lymphocytes
10. Helper T cell response
11. Lymphokines and cytokines
12. Lymphokines and cytokines
13. Properties of antibodies – antibody and antigen bindings
14. Response of B cells to antigen
15. Plasma cells and memory cells production and function
16. The genetic basis of antigen recognition
17. Mid-Semester examination
18. Antigen - antibody reactions
19. The complement fixation – regulation of complement systems
20. Immunoglobulin - types, distribution and synthesis
21. Molecular biology and functional diversity of antibodies
22. Antigenic determinants

23. Isotypes, allotypes and idiotypes
24. Monoclonal antibodies - history and scope
25. Hybridoma technology
26. Resistance ot tumors – Tumor immunotherapy
27. Acute inflammatory response
28. Tolerance – T cell tolerance , B cell tolerance and duration of
tolerance
12
29. Regulation of immune response 
30.Transplantation and
vaccination
– 
31.Hypersensitivity,Auto Breakdown in self im m unity
tolerance. 32. The phylogeny of immune systems 
33.
Immunotechnological applications
34.Review ofclasses
Practical schedule
1. Symptoms of virus diseases and preparation of buffer 2. Transmission
of virus - Mechanical, Vector
3.Physicalpropertie
proteins
5. Serological tests 
6.S erologicaltests .
7
Preparation of antigen
9.Raring ofan
methods of bleeding animals 10. Preparation of serum and
complement 
11.Antigen
- antibody reactions 
12.E LIS A 
13.P
test
14.Im - Immunoelectrophoresis m unodiffusion
15.Com plem en
test .
16.Affinity chrom atograp
Suggested readings 
E rt,K.D. lge 1996. Immunology -Understanding the
immune system. Wiley - Liss, New york.p.468. Goldsby, R.A., T. Kindt.,
B.A. Osborne and J. Kuby, 2002. Immunology. W.H.Freeman and
Company, New York p.551. 
M atthew s,R .E .F .1

plant virology, Academic Press,. New York p.403. 
R oitt,I.M .1971.
Essential Immunology. Blackwell Scientific Publishers, Oxford.
P.448.
Streips,U.N.an
Wiley – Liss. John Wiley & sons, Inc., NY.
Tizard,I.R.2008.
Immunology – An Introduction 8 th Edn, Saunders College Publishers, New
York
Turner.1994
The biology of viruses, Mc Graw - Hill, Singapore p.408.
2.2. AGM 607 BACTERIAL DIVERSITY (2+1)
Objective 
E tionary volu survey and characteristics of bacteria focusing on
autotrophic and heterotrophic prokaryotes from various habitats. Isolation,
examination, and identification of bacteria from field collections using
microscopic, physiological, biochemical, molecular, phylogenetic, and
computer database techniques.
13
Unit I
Introduction -Microbial Life ofm and etabolic The Evolution diversity
of the Earth – origin of life - Classical and Modern Approaches to
Prokaryotic Taxonomy-Microbial Diversity - Diversity in the environment –
How do we know-Detecting microbes and their activities in soil, water.
Unit II
M -Molecular orphologicalDiversity
characterizations of organisms -
Overview of phylogenetic diversity - Principles of molecular phylogeny -
Unusual Microbial Habitats, hot springs hydrothermal vents, mine tailings.
Describe microbial diversity in various natural environments including
extreme environments and anoxic habitats; functional biodiversity of
microbes, Mechanism of survival and metabolic adaptations in
prokaryotes.
Unit III
M - Anaerobic etabolic Diversity horizons – fermentations and
hydrogen – Syntrophy - Aerobic organotrophs -the facultative aerobes -
Aerobic chemolithotrophs - The photosynthetic way of life, oxygenic and
unoxigenic - Metabolism: Energy, Enzymes and Regulation -Major groups
of environmentally important bacteria are covered, with a focus on the
importance of metabolism in determining an organism's role in nature.

Unit IV
Phylogenetic - An Overview - Diversity Archaea - Physiological
Types– Phylogeny - Bacteria – Proteobacteria - Bacteria - Gram+ Bacteria
- Bacteria - Cyanobacteria & Other Phyla- isolate, cultivate, and classify
prokaryotic microorganisms - Use aerobic and anaerobic techniques to
isolate and cultivate prokaryotes from natural and man-made
environments.
Unit V
- 
O verview ofgenom ic d
Concept of microbial species diversity and DNA-transfer: mechanisms -
DNA transfer in physiology - islands and modules DNA transfer in
evolution – lateral transfer - horizontal gene transfer and microbial
evolution - Molecular Phylogeny - Analyze DNA sequences to identify
prokaryotes using molecular databases and phylogenetic software.
Practical
W - Enrichment inogradsky of Colum Thermophiles n - Isolate
Bacteria from wetland - Isolation of Radiation Resistant Bacteria -Isolation
of Anoxygenic Phototrophic Bacteria Selection and Isolation of
Streptomyces - Isolating Iron-Oxidizing Bacteri- Soil Hetetrotrophic
Bacteria - Anaerobic techniques - Media Preparation and Dispensing -
Hungate Roll Tube technique - Sulfate-Reducing Bacteria: Enrichment
Culture,Isolation - Methanogen : Enrichment Culture, isolation - PCR
technique -Molecular Phylogeny.
Lecture Schedule
1. Introduction to metabolic diversity
2. Microbial life and the evolution of the earth
3. Classical and modern approaches to prokaryotic taxonomy
4. Bacterial diversity - a changing paradigm
5. Morphological diversity
6. Molecular characterizations of organisms

7. Overview of phylogenetic diversity
8. Principles of molecular phylogeny
9. Unusual microbial habitats
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10. Metabolic diversity
11. Anaerobic horizons – fermentations and hydrogen
12. Anaerobic horizons – syntrophy
13. The photosynthetic way of life
14. The photosynthetic way of life, cont.
15. Diversity in the environment – how do we know
16. Detecting microbes and their activities
17. Mid-semester exam
18. The geothermal way of life
19. Mechanisms of thermal stability
20. Phylogenetic diversity - an overview
21. Archaea - physiological types
22. Archaea – phylogeny
23. Bacteria – proteobacteria
24. Bacteria – proteobacteria

25. Bacteria - gram+ bacteria
26. Bacteria - cyanobacteria & others
27. Overview of genomic diversity: technology and organisms
28. Genomic diversity – cont
29. Concept of microbial species
30. Diversity and DNA-transfer: mechanisms
31. DNA transfer in physiology
32. DNA transfer in evolution – lateral transfer
33. Molecular phylogeny
34. Recap.
Practical Schedule
1. Winogradsky column
2. Enrichment of thermophiles
3. Isolation of bacteria from wetland
4. Isolation of radiation resistant bacteria
5. Isolation of anoxygenic phototrophic bacteria
6. Enrichment and isolation of Streptomyces
7. Isolating Iron-oxidizing bacteria
8. Soil hetetrotrophic bacteria

9. Anaerobic techniques - media preparation and dispensing
10. Hungate Roll Tube technique
11. Sulfate-reducing bacteria: enrichment culture
12. Isolation of sulfate-reducing bacteria
13. Methanogen : enrichment culture
14. Methanogen isolation
15. PCR technique
16. Molecular phylogeny
17. Practical examination
Suggested readings
Anthoney, C. 1988. Bacterial Energy Transduction. Acadmic Press, New
York. 
Hopwood,D.A.and K.
Diversity. Academic Press, New York. Madigan, M.T., J.M. Martinko, P.V.
Dunlap, D.P.Clark. 2008. Brock Biology of Microorganisms Twelfth Edition,
Prentice Hall, Inc., New Jersey.
15
Moat, A. G. and J. W. Foster. 1995. Microbial Physiology, John Willey and
Sons, New York. Zehnder, A. J.B. 1988. Biology of Anaerobic Bacteria.
John Wiley and Sons, New York.
B orkin, alow W. s,A .,H .G .T rup
Harder and K. H. Schleifer. 1991. The Prokaryotes: A Handbook on the
Biology of Bacteria, Ecophysiology, Isolation, Identification, and
Applications, 2 nd editions. Springer Verlag, New York.
Priest, F.G., A. Ramos-cormenzana and B.J.Tindall. 1994. Bacterial
Diversity and Systematics. Springer-Verlag, New York

Outcome
microbial diversity in various natural environments including extreme
After com pleting
environments such as hyperthermal, hypersaline, and anoxic habitats
•Evaluate approaches to isolate, cultivate, and classify
prokaryotic microorganisms
•Use aerobic and anaerobic techniques to isolate and
cultivate prokaryotes from natural and 
 man-made environments
•Analyze DNA sequences to identify prokaryotes using
molecular databases and 
 phylogenetic software 
 2.3. AGM 608
Advanced Methods for Identification of Microorganisms (2 + 1)
Objective 
To understand basic conce
microorganisms in conjuction with 
 advancements in identifying
and classifying them.
To update students
tools in phylogeny and identification of microbes. 
 Unit I 
M olecular
coding and energy generation –origin of modern eukaryotesevolutionary
chronometers- Ribosomal RNA sequences and cellular
evolution. General principles of classification- - International Code
of Nomenclature of Bacteria-major developments in bacterial
classification- classification of prokaryotic organisms and concept of
bacterial speciation –Etymology in nomenclature of prokaryotes.
Unit II 
M orphological,
biochemical, metabolic, enzymic, reproductive and molecular
biological features for delineating prokaryotes from eukaryotes,
bacteria from archaea and Gram - ve bacteria from Gram+ve
bacteria- Isolation and characterization of anaerobes and
extrmophiles. 
 Unit III
Biochemical techniques: Instrumentation of GC/ Gs-MS - Cellular
fatty acid analysis (CFA), protein profile by SDS-PAGE, isozyme
pattern and zymogram analysis- Molecular taxonomy: GC content,
DNA / DNA hybridization, DNA/ RNA hybridization, 16S rRNA
sequence analysis –DNA finger printing. 
 Unit IV
Electrophoresis (PFGE), Restriction Fragment Length
-
M odern approaches to c
Pulsed Field G e

Polymorphism (RFLP) and Random Amplified Polymorphic DNA
(RAPD) – Microsatellite Markers – Ribotyping - phylogenetic
backbone for prokaryotic systematics.
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Unit V
Num – Adensonian ericaltaxonom method y of classificationpolyphasic
taxonomy – antigenic typing: ELISA and Radio immunoassayphage
typing – DNA probes and their application in Microbial Ecology –
culture collections as essential resources for Microbiology – patenting of
microbial cultures.
Practical
M l differentiation orphologicaland of eubaeteria cultura and
archaeobacteria, Gram +ve and Gram – ve bacteria - Biochemical
characterization of prokayayotes eubacteria and archaeobacteria, Gram
+ve and Gram –ve bacteria- intrinsic antibiotic suseptibitiy of prokaryotes
eubacteria and archaeobacteria; Gram +ve and Gram –ve bacteria;
Biochemical techniques for identification of bacteria; CFA, SDS –PAGE,
isozymes pattern and zymogram analysis-Molecular techniques for
identification of bacteria; G+C content, DNA-DNA hyhridization, DNA-RNA
hybridization RAPD, RFLP, dendrogram analysis, microsatellite markers
for strain identification – immunometric assay like ELISA /western blot,
radioimmunoassay for strain identification- Numerical taxonomy using
softwares.
Lecture Schedule
1. Evolution of earth and earliest life forms- primitive organisms:
2. Molecular coding and energy generation
3. Eukaryotes and organelles –origin of modern eukaryotes – evolutionary
chronometers-
4. Ribosomal RNA sequences and cellular evolution
5. General principles of classification-classification, nomenclature and

identification-
6. International Code of Nomenclature of Bacteria-
7. Major developments in bacterial classification-History of Bergey’s
Manual
8. Classification of prokaryotic organisms and the concept of bacterial
speciation-
9. Etymology in nomenclature of prokaryotes
10. Methods of classification-Conventional methods-prokaryotic
domains: morphological, cultural,
cytological,antibiotic
susceptibility
11. Biochemical, metabolic, enzymatic and reproductive characters.
12. Molecular biological features for differentiation of archebacteria from
eubacteria
13. Molecular biological features for delineating prokaryotes from
eukaryotes.
14. Morphological, cultural, cytological, antibiotic susceptibility,
biochemical, metabolic, enzymatic,
biological features for differentiation of archebacteria
reproductive and m
15. Morphological, cultural, cytological, antibiotic susceptibility,
biochemical, metabolic,
16. enzymatic, reproductive
17. Mid-semester Examination
18. Modern approaches to classification- Biochemical techniques ;

19. Cellular fatty acid (CFA) analysis, protein profile by SDS – PAGE,
20. Isozymes pattern and zymogram analysis
21. Molecular taxonomy: G+C content,
22. DNA / DNA hybridization, DNA / RNA hybridization.
23. 16S rRNA sequence analysis for phylogenetic classification
24. DNA fingerprinting: Pulsed Field Gel Electrophoresis (PFGE).
25. Restriction Fragment Length Polymorphism (RFLP).
26. Random Amplified Polymorphic DNA (RAPD)-
27. Microsatellite Markers – Ribotyping-Phylogenetic backbone for
prokaryotic systematics
28. Numerical taxonomy – Adensonian method of classification
29. Antigenic typing of microorganisms:
30. ELISA and Radio Immunoassay
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31. Phage typing
32. DNA probe and their application in Microbial Ecology
33. Culture collections as essential resources for Microbiology
34. Patenting of microbial cultures
Practical schedule
1. Morphological characterization of type cultures of eubacteria and

archeabacteria and Gram positive & Gram negative bacteria
2. Cultural characterization of type cultures of eubacteria and
archeaobacteria and Gram positive & Gram negative bacteria
3. Biochemical methods for identification of type cultures of Gram + &
Gram –bacteria
4. Antibiotic susceptibility of Gram + & Gram –bacteria
5. GC based fatty acid analysis for species differentiation in Gram + &
Gram –bacteria
6. Isozyme pattern by SDS-PAGE and Zymogram analysis of bacterial
cultures
7. Isolation of genomic DNA from bacterial cultures and estimation of G+C
content
8. DNA-DNA hybridization using DIG-OXIENIN system
9. DNA-DNA hybridization using DIG-OXIENIN system
10. RFLP-PCR for sequence analysis and characterization of type
cultures
11. RFLP-PCR for sequence analysis and characterization of type
cultures
12. RAPD-PCR and dendrogram analysis of bacteria cultures
13. RAPD-PCR and dendrogram analysis of bacteria cultures
14. Identification of Microbiol cultures by ELISA
15. Western blot analysis of microbial type cultures

16. Identification of Microorganisms by Numerical taxonomy using
softares
17. Practical Examination
Suggested readings
Balows, A., H. G. Truper, M. Dworkin, W. Harder and K. H. Schleifer. 1991.
The Prokaryotes, 2 nd edition. Springer- Verlag, New York. 
H il,D .R .1978
A Dictionary of Microbial Taxonomy, Cambridge University Press,
Cambridge. Holt, J. G. 1984-1989. Bergey’s Manual of Systematic
Bacteriology, 1 st Ed., Vols. 1-4, The Williams & Wilkins Co., Baltimore,
USA.
Logan, N. A. 1994. Bacterial Systematics Blackwell Scientific Publications,
Oxford.
M 1985. acario,A.J.I.and Monoclonal E.Conway de M a
Antibodies against Bacteria, Vol. II. Academic Press, Orlando. 
M adigan,M .
T. , J. M. Martinko and J. Parker. 2000. Brock Biology of Microorganisms
Ninth Edition. Prentice Hall, Inc., Saddle River, NJ.
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