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Department of Agricultural Microbiology

COURSE OUTLINE (Choice Based Credit System)

M.Sc.(Ag.) Microbiology

Faculty of Agricultural Sciences Aligarh Muslim University

Aligarh – 202002 May 23, 2015

Course Structure of M.Sc. (Ag.) Microbiology

Paper Code

Title Credit Marks

I-SEMESTER Sessional /

Assignment Mid

Semester End

Semester M. Marks

MBM-1001 General Microbiology 3 10 30 60 100 MBM-1002 Soil Microbiology & Biochemistry 3 10 30 60 100 MBM-1003 Biomolecules 3 10 30 60 100 MBM-1004 Food Microbiology 3 10 30 60 100 MBM-1005 Introduction to Immunology 2 10 30 60 100 MBM-1071 Lab Course 4 10 30 60 100

II- SEMESTER MBM-2001 Microbial Physiology & Metabolism 3 10 30 60 100 MBM-2002 Microbial Ecology 3 10 30 60 100 MBM-2003 Industrial Microbiology & Fermentation

Technology 4 10 30 60 100

MBM-2004 Molecular Biology and Microbial Genetics 4 10 30 60 100 MBM-2071 Lab Course 4 10 30 60 100

III- SEMESTER MBM-3001 Biofertilizer and Biopesticides 3 10 30 60 100 MBM-3002 Genetic Engineering and Tissue Culture 4 10 30 60 100 MBM-3003 Environmental Microbiology & Organic

Waste Management 3 10 30 60 100

MBM-3071 Lab Course 4 10 30 60 100 Elective-I (DC) *** MBM-3011 Pathogenic Microbes 4 10 30 60 100 MBM-3012 Computer Applications in Agriculture 4 10 30 60 100 MBM-3013 Biodegradation and Bioremediation 4 10 30 60 100 Ability Enhancement (DC) MBM-3072 Seminar 4 - - 100 100 Open Elective PPM-3023 Insect Pest of fruits and vegetable crops 2 10 30 60 100 PPM-3091 Biological control 2 10 30 60 100

IV- SEMESTER MBM-4001

Methods in Applied & Molecular Microbiology

4 10 30 60 100

MBM-40D1 Project Work and Dissertation 10 - - 100 100 Elective-II (DC) *** MBM-4011 Microbial Bioresource & Agro-

nanotechnology 4 10 30 60 100

MBM-4012 Current Trends in Agricultural Microbiology 4 10 30 60 100

MBM-4013 Biostatistics and Bioinformatics 4 10 30 60 100 Ability Enhancement (DC) MBM-4072 Seminar 4 - - 100 100 MBM-4073 Field work / Self study 4 - - 100 100 Total credits 96 2600

* Course code will be provided by Controller’s office. ** Courses from the Department of Plant Protection, F/O Agricultural Sciences. *** Select any two courses from Elective (DC) – I and II, in semester III and IV, respectively.

Summary:

Core course 64 160 480 1060 1700

Elective 16 40 120 240 400

Ability Enhancement 12 ----- ----- 300 300

Open Elective 04 20 60 120 200

Total credits 96 220 660 1720 2600

I – SEMESTER

MBM1001, GENERAL MICROBIOLOGY Objectives: This course of General Microbiology has been developed for students with the objective to cover the ‘Basics of Microbiology’ starting from the historical perspective to the current status in the subject. It is a very comprehensive syllabus encompassing all fundamentally important aspects which will help building a strong foundation in Microbiology.

Sessional/Assignment: 10 Marks

Mid Semester: 30 Marks End Semester: 60 Marks

M. Marks: 100 Credits: 03

Unit-I

History and development of Microbiology-Landmarks in Microbiology, Theory of abiogenesis & biogenesis, Discovery of microscope and microbes: Bright field, Fluorescence, Confocal laser Scanning microscopy, Electron Microscopy, Koch’s postulates, River’s postulate. Study of microbes – Development of laboratory techniques, pure culture and culture characteristics. Microbial growth Cycle, mathematics of exponential growth, Direct and indirect measurement of bacterial growth, Microbial growth at Low and High temperature, Factors affecting microbial growth: pH, osmolarity and oxygen, Culture dependent and independent analysis of microbial communities. Classification and Nomenclature of Microorganisms – Microbial taxonomy: classical taxonomy, recent development in microbial taxonomy including, GC ratio, DNA: DNA Hybridization, Evolutionary Chronometers: RNA based phylogenetic analysis, Ribotyping, Multilocus sequence typing, Fatty Acid Analysis (FAME), Bacterial speciation.

Unit-II The bacterial cytology – cell components, Paracrystalline surface layers, cytoplasmic membrane, structures of bacterial cell external and internal to cell wall, Prokaryotic genome, osmotic control, Biosynthesis of peptidoglycan, Cellular inclusions and gas vesicles, Flagella and Motility, Chemotaxis, Bacterial spore: Process of sporulation & germination. Bacterial Diversity: General, morphological, cultural and biochemical properties of Rickettsia Mycoplasma and Actinomycetes, Cyanobacteria, Chlamydia, Cytophaga, Nanoarchaeum. Fungi, Algae and Protozoa-Distinguished characteristics of fungi, general account on morphology, reproduction, physiology and classification. Filamentous Fungi, Macroscopic Fungi, Unicellular Fungi, Algal Diversity life cycle and importance of protozoa. Viruses- General characteristic features of plant, animal and bacterial viruses- General properties, morphology and reproduction mechanisms.

Unit – III Bacterial Nutrition: Major nutritional types of bacteria, Microbial requirements of C, N, S, P, and microelements, growth factors, etc. Preparation and use of culture media. Control of microorganism: Physical and chemical methods. Identification & Preservation methods of microbes. Safety in Microbiology Laboratory: Biological Containment and Laboratory Biosafety levels. Diseases and Resistance to disease in plant and animal: Common causative agent and their pathogenicity, Concept of prevention and treatment of microbial diseases, Antibiotics: classification mode of action and development of antibiotic resistance in bacteria. Suggested Reading:

Microbiology by Michael J. Pelczar et. TaTa McGraw Hill Publisher Company Ltd.(2002) Brock Biology of Microorganisms by Madigan and Martinko, Pearson Education International (2006) Microbiology by Davis et. Al. Harper & Row Publishers (1980) Text book of Microbiology by Ananthanarayanan & Paniker, Universities Press(2010) Microbiology by Black J.G., John Wiley & Sons, INC.(2008) Alcamo Fundamentals of Microbiology by Pommville J.C., Jones & Bartlett Publishers (2011) Microbiology : Principal and Exploration 6th 7th edition JG black John Wiley & Sons,(2007) General Microbiology 5th edition Roger Y Stanier, ML Wheelis and PR Painter , MacMillan Press Ltd.(2005) Microbial Ecology : Fundamentals and Application (4th edition) Ronald M. Atlas and Richard Bartha,

Pearson Education International (1998)

MBM-1002, SOIL MICROBIOLOGY AND BIOCHEMISTRY Objectives: This paper of microbiology and biochemistry of soil is designed with the objective to provide general introduction of soil and in depth information on soil microbial diversity and the role of microorganisms in biogeochemical cycling of elements like C,N,P and trace elements and soil fertility. The course also includes the methodology and technical aspects to provide comprehensive knowledge of the subject.




Unit-I

Definition and composition of soil, soil structure and characteristic features, Soil as substrate for growth of microorganisms. Role of humus and clay in ion exchange and nutrient availability. Diversity of soil microorganisms, their occurrence, characteristic features and role. Methods of studying soil microorganisms: culture dependent and independent methods- Soil enzymes as indicators of soil health. Carbon cycle, aerobic decomposition of native and added organic matter, lignolytic and cellulolytic microorganisms.

Unit-II Nitrogen cycle: microbiology and biochemistry of Ammonification, nitrification and denitrification, utilization of various nitrogen sources. Nitrogen fixation, diversity of diazotrophs, associative and symbiotic Nitrogen fixation. Mechanism of nodulation and nitrogen fixation, role of various genes in these processes. Nitrogenase protection mechanism in diazotrophs, future prospects for increasing symbiotic nitrogen fixation.

Unit-III Microbial transformation of Phosphorus—Phosphorus cycle, Source of organic and inorganic phosphates in soil and elsewhere, mineralization of inorganic phosphates, factors affecting phosphate solubilization and mechanism, Microbial transformation of sulphur- Sulphur cycle, Source of sulphur, sulphur oxidizing and reducing microorganisms (Thiobacillus and Desulfovibrio), biochemistry of transformation. Sulphate and Sulphur reduction, H2S formation, Role of Thiobacillus in agriculture and soil reclamation. Microbial transformation of Iron, Manganese, Zinc, Copper and Potassium. Suggested readings:

Soil microbiology and Biochemistry by EA Paul and F.E. Clark, Academic press (1989) Soil microbiology Ecology and Biochemistry by EA Paul Academic press,IIIrd Edition (2007) An introducation to Soil Microbiology (wiley Publication), Martin Alexander (1986) Microbiolgy Ecology: Fundamental & Applications by Atlas & Bartha (2005) Methods in Applied Soil Microbiology and Biochemistry by A.Kassem & N. Paolo, AP Ltd. (1995) The Nature and Properties of Soils by Brady N.C.Prentice Hall of India Pvt.Ltd. (1996) Soil Microbiology by Subba Rao Oxford & IBH Publishers (2008) Soil Microorganisms and Plant Groth by Subba Rao Oxford & IBH Publishers (1995) Soil Fertility and Fertilizers by Tisdale et.al. (2003)Prentice Hall of India Pvt.Ltd.

MBM-1003, BIOMOLECULES

Objectives: With the aim to provide comprehensive information to the students about the structural and functional diversity of biomolecules in the living system, and their significance in cell structure physiology and genetics.

Sessional/Assignment: 10 Marks Mid Semester: 30 Marks End Semester: 60 Marks


Unit-I

Definition, classification, structure and functions of carbohydrates, Stereoisomerism, aldoses and ketoses. Important classes of monosaccharide’s disaccharides, Structure of polysaccharides and muco-polysaccharides. Definition and classification of lipids. Nature of fatty acids. Role of triglycerides in energy storage and phospholipids in membrane formation, sterols.

Unit-II

Nature of naturally occurring amino acids, classification, structure and properties, Structure and functions of proteins (primary, secondary, tertiary and quaternary structure). Forces responsible for maintenance of protein structure. Protein denaturation and Folding, Molecular chaperones molecular breathing in protein, Basics of protein-ligand interactions, General idea of role of protein as hormones and antibodies. Fat soluble and water soluble vitamins, elementary ideas about the physiological function and deficiency diseases. Role of water soluble vitamins as co-enzyme precursor.

Unit-III Basics of Nucleotides and Nucleic acids: Structure and function of nucleosides, nucleotides, polynucleotides. Composition of nucleic acids (ribo and deoxyribonucleic acids). Structure and function of DNA and RNA. RNA types and their functions, DNA supercoiling, Bacterial DNA, Chromatin structure and Nucleosomes. An Introduction to enzyme, Enzyme active site, Basics of regulatory enzyme, Enzyme inhibitors (competitive and non-competitive)

Suggested Readings:

Outlines of Biochemistry by Conn & Stumpf, John Wiley & Sons Lehninger Principles of Biochemistry by Lehninger by Cox et. Al. (2010) WH Freeman and company Biochemistry by Stryer WH Freeman and company Biochemistry (Seventh Edition) JM Berg and JL Tymoczk and L.Stryer (international Edition) W.H. Freeman

& Company (2003) Biochemistry Rawn JD, Panima Publishing Co. (2004) Outline of Biochemistry EE conn, Paul K Stumps et. al, John Wiley & Sons(1987) Practical Biochemistry Principal and Technology, K.Wilsone and John Walker, Cambridge University Press

(2004)

MBM-1004, FOOD MICROBIOLOGY

Objectives : Food Microbiology provides a basic understanding of different foods and its spoilage. Further, it also helps to better understand the mode of food preservation and how the quality of different foods can be preserved following the various international guidelines.




Unit –I

Food and their composition, source, type and role of microorganisms – Psychrophiles, osmophiles, halophiles, thermophiles, pH-tolerance and spore formers. Food Spoilage- Causes of spoilage and spoilage of canned food, classification of foods by ease of spoilage, Factors affecting the growth of microorganisms in food. Chemical changes caused by microorganisms.

Unit-II Microbial flora and spoilage of meat, fish, fish products, eggs, milk and milk products, fruits, vegetables, juices and bakery products. Fermentation of pickles, sauerkraut and idly. Single cell protein, Methods of food preservation- General principles of preservation by use of chemicals, high temperature, low temperature and irradiation and drying processes. Aseptic packaging materials.

Unit-III

Food sanitation, control and inspection. Detection of microorganisms in food: indicator organism, Food poisoning and food infections, Food borne diseases their causative agents and control measures. Food quality and assurance: Quality control parameters of various foods with special reference to microbiological quality. Good manufacturing practices (GMP), HACCP Importance of microbiological quality during food processing and packaging. Microbiological standards and guidelines and food laws. Suggested Readings: Basic Food of Microbiology by Banwart G.J. CBS Publishers & Distributors (2002) Food Microbiology by Frazier and Westhoff TaTa McGraw Hill (2005) Modern Food Microbiology by jay et.al. Springer India Ltd. (2006) Food Microbiology: Fundamentals and Frontiers by Doyel et.al. ASM Press (2001)

MBM-1005, INTRODUCTION TO IMMUNOLOGY

Objectives : Introduction to Immunology attempts to provide an introductory broad canvas of immunology. The course will cover the theory and techniques in immunology, encompassing the structure and function of immunoglobulin’s and immunological methods for developing a basic understanding of the Subject.



Unit –I

General concept of immune responses- T and B cells, Antigens; definition, classes and immunologic properties, Haptens, Mitogens, and Epitopes. The role of macrophages, Humoral and cell mediated immune responses. Antibody – Definition, Basic and fine structure of immunoglobulin’s, Antigenic determinants of immunoglobulin- Isotypic, allotypic and Idiotypic determinants, Immunoglobulin isotypes and their function. Theories of antibody formation- Selection and Clonal selection theory.

Unit-II Antigen-Antibody interactions- Antibody affinity, Antibody avidity, Precipitin reaction in fluids and gel, Agglutination reaction. Serological methods: Immunodiffusion (Mancini and Ouchterlony method), Immunoelectrophoresis, RIA, ELISA, Immunofluorescence. Hybridomas and Monoclonal Antibodies-Formation and selection of hybrid cells, Principal of monoclonal antibodies production, Application and advantages of monoclonal antibodies. Suggested Readings: Essential Immunology by lvan Roitt Blackwell Science (1997) Immunology by Janis Kerby, W.H.Freeman & Co.(2003) A practical Guide to Monoclonal Antibodies by Liddel J.E.& Cryer A. John Wiley & Sons The ELISA Guidebook by Crowther J.R. Human Press (2009) Microbiology by Michael J.Pelczar et. al. TaTa McGrew Hill Publisher Company Ltd. (2002) Microbiology by Davis et. al. Harper & Row Publishers (1980)

MBM-1071, LAB COURSE



Preparation and use of media, Grams staining, Culture and microscopic examination of bacteria, fungi and actinomycetes, Enumeration of microorganism from soil samples, Decomposition of organic matter in soil CO2 evolution, Carbon estimation, Cellulose and pectin decomposing microorganisms in soil, Microbial biomass, fractionation and estimation of soil humus, Isolation of Rhizobium from nodules, Cultural tests to distinguish Rhizobia from contaminants, Nodulation tests , Survival of Rhizobium on seed and in soil Isolation of Azotobacter chroococcum and Beijerinckia. Microbiological examination of water, milk and milk products, Detection of carbohydrates, proteins, amino acids by colour reaction, Colorimetric estimation of glucose by glucose oxidase/peroxidase also in biological samples (Fruits),Separation of plant pigments by column chromatography, Immunological techniques. Field work.

II-SEMESTER

MBM-2001, MICROBIAL PHYSIOLOGY AND METABOLISM Objectives: This course attempts to highlight the concept and mechanistic aspects of bacterial growth nutrition and metabolism. The course covers the important metabolic pathways related to synthesis, degradation and regulation of biomolecules in cell.




Unit-I

Introduction and scope of microbial physiology, Microbial nutrition and growth, Synchronous and Continuous culture, Diauxic growth. Autotrophic nutrition of microorganisms. Mechanism of nutrient transport in microorganisms. Microbial polysaccharides. Chemical nature, synthesis and functions. Bacterial and plant photosynthesis: Historical perspective, light and dark reaction and their energetic. Oxygenic and anoxygenic photosynthesis.

Unit-II Aerobic and anaerobic metabolism in bacteria Catabolic reaction of anaerobic chemohetrotrophs, Methods of study of intermediary metabolism: role of ATP, reducing power and precursors metabolites in metabolism, substrate level and oxidative phosphorylation, Biochemistry of catabolic reactions in aerobic heterotrophs: Glycolytic, hexose monophosphate shunt and Entner-Doudoroff pathways, TCA cycle, electron transport chain and oxidative phosphorylation.

Unit-III Role of glyoxylate cycle in acetic acid oxidation, special pathways for primary attack on organic compounds by microorganisms, Oxidation of fatty acid (B-oxidation) and certain amino acids, Gluconeogenesis. Biosynthesis and degradation of nucleotides. Anaerobic respiration and fermentation. Regulation of metabolic pathways Suggested Readings:

Bacterial Metabolism by Doelle, H.W. Academic Press (2005) Microbiology by Davis et. al. , Harper & Row Publishers(1980) General Microbiology by Stainier et. al. MacMillan Press Ltd.(2005) Microbiology by Michael J. Pelczer et. al. TaTa McGraw Hill Publisher Company Ltd. (2002)

MBM-2002, MICROBIAL ECOLOGY

Objectives : This course has been designed to impart knowledge about some fundamental aspects of ecology. This course focus on to understanding the needs of interaction occurring among microbes in nature and their consequential impacts on healths.




Unit-I

Microbial ecology – Concept of habitat and ecological niches, Ecosystem, Energy flow, food chain, food web, biotic community concept, Microbial Succession, adaptation and natural selection of microbial population, Ecology of algae.

Unit-II Microbial interactions – Symbiosis, Synergism, Commensalism, Ammensalism, Predation and Parasitism, Mycorrhizal associations- structure, characteristics mechanism and their role in Agriculture and Forestry, Algal association with other microorganisms and plant. Endophytic associations of microbes with plants and its significance.

Unit-III

Microbial Colonization of plant surfaces- The rhizosphere and colonization, plant root exudates and their characteristics, Nutrients and plant community productivity, Influence of plant rhizosphere effect, Phyllosphere associated microflora and their role, Phytoalexin-Properties and induction. Microbial biofillm. Associated with plant surfaces and their significance. Suggested Readings:

Microbial Ecology : Fundamentals and Applications by Atlas & Bartha, Pearson Education (2005) Environment and Pollution by R.S. Ambasht, CBS New Delhi (2005) Soil Microbiology, Ecology and Biochemistry by Paul E.A. Academic Press (2007) Microbial Ecology: An Evolutionary Approach by Mc Arthier, J.V. Academic Press (2006) Experimental Microbial Ecology Richard G Burns, JH Slater Blackwell Scientific Publisher Oxford (1982) Biotechnology of Plant – Microbe Interactions (Environmental Biotechnology ) James P. Nakas

MBM-2003, INDUSTRIAL MICROBIOLOGY & FERMENTATION TECHNOLOGY

Objectives: The paper industrial microbiology and fermentation Technology is specially developed to expose and train students on applied aspects of microbiology in industry and the basic technology used in fermentation to obtain microbially derived products such as pharmaceuticals, medical and human health related products. Current strategies used in industry to develop microbial strain to increase productivity and scale up of fermentation process has been covered.




Unit-I

Definition of primary and secondary metabolites, screening of new metabolites and isolation approaches of unidentified microbial products. Methods of strain development for industrial purposes: mutation, recombination, protoplast fusion, regulation and gene technology. Substrates used as carbon and nitrogen source for industrial fermentation. General concept of microbial fermentation; Unit operation in product recovery.

Unit-II Fermentation technology: Methods of fermentation, Growth kinetics of microorganisms during fermentation General design of fermenter, concept and importance of gas exchange and mass transfer and scale-up in microbial fermentation. Processes of fermentation. Basic concept of cell and enzyme immobilization and reactors used for immobilized enzymes.

Unit-III Microbial production of ethanol, citric acid acetic acid. Fermentation of antibiotics (Penicillin and semisynthetic penicillin), enzymes (Amylases, Glucose isomers, Proteases, Penicillin acylases), Amino acids and Vitamins (Riboflavin & Vit B-12). Industrial production of amino acids by fermentation.

Unit-IV

Production of yeast and yeast derived products and Single Cell Protein. Industrial production of alcoholic drinks (wine , bear etc.) biotransformation; Principle and application in industry, Role of microbes and microbial enzymes in the fermentation of tea, coffee and cocoa and production of silage. Suggested Readings :

Biotechnology : A text book of Industrial Microbiology (second edition) by W. Crueger and A. Crueger, Science Tech. Publisher USA (1989)

Practical Biochemistry Principle and Technology , K. Wilson and John Walker 2004 Cambridge University Press

MBM-2004, MOLECULAR BIOLOGY AND MICROBIAL GENETICS

Objectives: This paper is designed specially to introduce a comprehensive course with basic concept of molecular biology and its application in studying microbial genetics and to understand molecular mechanism of gene expression and regulation.




Unit-I

DNA replication in prokaryotes, Basics of eukaryotic DNA replication, Transcription, Post – transcriptional modification of RNA. Eukaryotic cell cycle: cell cycle regulation and checkpoints. The Nucleolus: Nuclear envelope, nuclear pores, nuclear localization signals, Genetic code, Expression and regulation of bacterial gene, Lactose and tryptophan operons.

Unit-II Gene transfer in bacteria – conjugation, transformation and transduction, gene mapping and sequencing of DNA. Mobile DNA, Plasmids and episomes, Determination of plasmid replication, maintenance, stability and copy number, plasmid incompatibility. (Inc P, N, W, Q,), MOB-Typing, Bacterial variation and population genetics (Dynamics). Mutation-Types of mutations, Molecular basis of mutation, Site-directed mutagenesis.

Unit-III Replication of single and double stranded nucleic acids of bacterial viruses. Phages of bacteria (Lytic & Lysogenic phages): Mechanism of infection, One-step growth curves of bacteriophages, Genetic regulation of lytic and lysogenic pathways. Oncogenes and protooncogenes.

Unit-IV Protein synthesis, Post translation modification of proteins. RNA editing; mRNA stability, Cell signaling, signal transduction and Apoptosis (programmed cell death), DNA repair-mechanisms that safeguard DNA in prokaryotic and eukaryotic systems. Basic concepts of proteomics. Molecular genetics of Cyanobacteria and Mycoplasma (Mollicutes). Suggested Readings: Genes IX by Benjamin Lewin, John and Barklet Publishers (2008) The Cell- A Molecular Approach by Cooper and Hausman, ASM Press (2004) Microbiology by Davis et. al. Harper & Row Publishers (1980) Molecular Biology of the Gene by Watson et. al., Benjamin Cummings (2013) Microbial Genetics by Freifelder D, Narosa Publishing House (1987) Principal of Genetics (8th edition) E.J Gardner, M.J.Simmon, DP Sustand, John Wiley and Sons (1991) Lehninger Principles of Biochemistry by Lehninger by Cox et. al, WH Freeman and Company (2010) Biochemistry by Stryer WH Freeman and Company




Biochemical activities of microorganisms (sugar fermentation and other biochemical tests), Measurement of bacterial growth/growth curve, Effect of environmental factor on bacterial growth. Assays of antibiotics/ enzymes/pigments, Enumeration of phyllosphere/rhizosphere microbial flora, Experimental work on nitrogen cycle,i.e. ammonification, nitrification and denitrification, Enumeration/Isolation of PSB/PSF and testing for their efficiencies to solubillze different type of insoluble phosphate, Transformation of sulphur compounds by Thiobacillus spp. And their characteristics, Cultivation and enumeration of bacteriophages, Lysogenic conversion, UV-induced mutagenesis in bacteria/ bacteriophages, Estimation of DNA by diphenylamine method, Bacterial conjugation. Educational tour to Agriculture Institutes/ Universities. Filed work.

III-SEMESTER

MBM-3001, BIOFERTILIZER AND BIOPESTICIDES

Objectives: This course has been developed with the specific objective to acquaint and enrich the students with the knowledge on basic and applied aspects of microbial inoculants production and their impact on crop production and protection of plant health against insect pests.



Unit-I

Definition and status of biofertilizer, types of biofertilizers, Nitrogenous and phosphatic biofertilizer Rhizobium, Azotobacter, Azospirillum, PSB/PSF (Pseudomonas striata, Bacillus Polymyxa, Bacillus megaterium, Aspergillus awamori and Penicillium spp.) Technologies for the production of biofertilizers. Quality control of biofertilizer. Methods of inoculation on seed and in soil. BIS standards of biofertilizers and its economics, Field programme of biofertilizers.

Unit-II

Bluegreen algae (Cyanobacteria) and their phages, characteristic of BGA and their role in nitrogen fixation. Algae as biofertilizers in rice cultivation, Azolla as biofertilizer, mass cultivation of algae, algal single cell protein. Role of algae in municipal sewage waste treatment. Vermiculture and vermicomposting.

Unit-III

Mycorrhizas- VAM, synthesis of growth promoting substances. Isolation, characterization and mass propagation of VAM fungi, Problems and prospects. Role of biofertilizers in plant nutrition and integrated plant nutrient management (IPNM). Integrated plant pest management, concept and component of IPPM. Microbial pesticides – Bacillus thuringinesis, structure of BT Toxin and their mode of action. Fungal and viral based biopesticides. Production technology for BT and Baculovirus based pesticide. Genetic improvement of Baculovirus for pesticide preparation. Advantages and limitations of biopesticides. Suggested Readings :

Phosphate Solubilizing microorganisms as Biofertillizers by Gaur A.C., Omega Scientific Publishers, New Delhi (1990)

Handbook of Microbial Fertilizers by Rai M.K. IBDC, Lucknow(2006) Biofertilizers for sustainable Agriculture by Sharma A.K.Agrobios, India (2005) Recent Advances in Biofertilizer Technology by Yadav et.al. SPURT, New Delhi (2001) Botanicals and Biopesticides by Parmar and Dev Kumar, Westnil Publishing House (1993) Bacterial Signaling by Reinhard Kramer Kristenjung, Wiley Blackwel Publisher (2010)

MBM-3002, GENETIC ENGINEERING AND TISSUE CULTURE Objectives: This course is essentially designed to provide comprehensive information on recombinant DNA technology, plant tissue culture and application of tissue culture techniques in development of transgenic plants.




Unit-I DNA cloning strategies in bacteria. Restriction enzymes, restriction and modification system, Characteristics of vector derived from bacterial plasmids, phage, plant and animal viruses. Selection vs screening of recombinant clones; Grunstein and Hogness method, Hybrid arrest and hybrid release translation, DNA sequencing, Yeast artificial chromosomes (YACs), Bacterial artificial chromosomes (BACs). Gene transfer to plants. Concept of transgenic plants.

Unit-II

Development and maintenance of plant tissue culture: tissue techniques, Plant cell culture, Plant tissue culture: callus culture, meristem culture, Organogenesis and embryogenesis, Plant organ culture; anther and pollen culture, Protoplast cuture, Adaptation of microbial techniques to plant tissue culture, Application of tissue culture for plant improvement. Techniques of plant breeding and its application in plant biotechnology.

Unit-III

Mass propagation, Micropropagation techniques, Cytoplasmic male sterility, In vitro fertilization and embryo rescue. Somatic hybridization, Somaclonal variations. Strategies of inserting gene into plants for development of disease and pest resistant, draught resistant and other types of improved varieties. Production of plant metabolites of medicinal and industrial applications.

Unit-IV Concept and application of stem cells; development and maintenance of animal tissue cultures and cell lines. Animal biotechnology and transgenic development. Plastome engineering and its application, metabolic engineering. Suggested Readings:

Biochemistry by Lubert Stryer WH Freeman and Company Microbiology by Davis et.al. Harper & Row Publishers (1980) Molecular Cell Biology by Lodish et.al. W>H> Freeman and Company (2002) Molecular Biotechnology by S.B. Primrose, Panima Publishing Corporation(2001) Principels of plant Biotechnology by Mantell, Matthews and McKee Lehninger Principles of Biochemistry by Lehninger by Cox et. al. WH Freeman and Company (2010) Molecular Biotechnology: Principle and Applications of Recombinant DNA by Grick B.R. Pasternak JJ, ASM

Press (2005) Agricultural Biotechnology by Purohit S.S. Agrobios India (2005) Genes IX by Benjamim Lewin John and Barklet Publishers (2008) The Cell- A Molecular Approach by Cooper and Hausman,ASM Press(2004)

MBM-3003, ENVIRONMENTAL MICROBIOLOGY & ORGANIC WASTE MANAGEMENT

Objectives:

This course has been developed with the objective to provide the comprehensive information on various aspects of environment contaminants and pollution indicators, environmental mutagenesis and environmental cleanup indicating organic waste recycling, sludge and water treatment approaches.



M. Marks:100 Credits: 03

Unit-I

Microbiology of air and aquatic environment including sea water- Bacteriological indicators of pollution, Bacteriological examination of water, nuisance bacteria in water systems. Chemical and microbiological characteristics, biological Oxygen Demand (BOD), Microorganisms and pollution problems and interaction with human bodies. Methods of detection of water borne pathogens. Human health risk assessment.

Unit-II

Environmental pollution: Definition, source and types of pollution (air, water and soil). Xenobiotic genotoxicity, Mutation detection by Ames microsomal assay. Microbial biotransformation / degradation of organic pollutants in soil including pesticides & hydrocarbons. Bioaccumulation and bioremediation, Biosensors, DNA probes and their environmental application, toxicogenomics.

Unit-III

Recycling of organic waste: Major sources of recyclable material including agricultural waste. Key technology in recycling of crop residues, human and animal wastes. Role of microbes in composting and biogas production Microbiology of biogas, Agricultural utilization of biogas sludge. Newer approaches to sewage treatment. Municipal solid waste treatment and management. Suggested Readings:

The Handbook of Water & Waste Water Microbiology by Mara D and Horan N.A Press(2003) Environmental Microbiology by Mitchell R. & JM, Niley Blackwell (2010) Bioresourse Ecology by Anantha Krishnan T.N. Oxford & IBH, P.Co. Pvt. Ltd. (1989) Soil pollution and soil organisms by Mishra P.C.APH Publishing Corporation (2008) Chemistry of Pesticides by Roy N.K. CBS Publishers & Distributors (2002) Biogas from Waste and Renewable Resources by Deublein D & Steinhauser A. (IIEdition ) Wiley- VCH

(2011) Wastewater Microbiology by Gabriel Bitton A John Wiley & Sons, Inc, Publisher




Production of biogas from agricultural wastes (animal waste/crop residues), Microbial examination of industrial waste water/sewage, Preparation of a few selected biofertilizer. Testing of specific biofertilizer for its quality, Methods of inoculation/seed bacterization, preparation of compost from organic waste, Estimation of C,N,P.etc.. of the prepared compost, Use of amendments (rock phosphate) and phosphate solubilizing fungi and nitrogen fixing bacteria. Cultural and morphological study of some important yeast and algae. Isolation of plasmid DNA from bacteria, Agarose Gel Electrophoresis of DNA, Protein Purification (partial) by Ammonium Sulphate precipitation, Gel electrophoresis of protein, Induction of enzyme in the Gram seed and its inhibition by cycloheximide. Quantitative estimation of protein, Carbohydrate, DNA and RNA. Toxicity assessment using bacterial system. Field work.

ELECTIVE-I

MBM-3011, PATHOGENIC MICROBES

Objectives : The objective of this paper is to provide an overview of the pathogenic microbes associated with human, animal and plants and their common principle of pathogenicity and general measures.




Unit-I

Microbial pathogens; bacterial pathogens, common pathogens to human and animals: microbial pathogenesis. Virulence and pathogenecity, microbial toxins, their mode of action. Host-microbe interaction, pathogenecity and control of common bacterial and fungal diseases.

Unit-II Fungal pathogens associated to human and animals. Classification and their pathogenicity, yeast moulds, superficial and systemic infection. Microbes with zoonotic importance, animal pathogens, epidemiology, dissemination and control.

Unit-III

Prophylaxis, vaccine and chemotherapy. Development of drug resistant in microbes. Viruses and their control. Common protozoal and viral diseases in animals and humans.

Unit-IV Phytopathogenic bacteria: Diversity, characteristic and mechanism of pathogenicity, Diseases caused and their control measures. Suggested Readings :

Microbiology – Michael J. Pelczar, JR. E.C.S.Chan Noel K. Krieg, Vth Edition (2005), Publisher – TATA McGraw Hill.

Plant Diseases – R.S. Singh, IXth Edition, Oxford and IBH (N. Delhi) Text Book of Microbiology – R. ananthanarayan, C.K. Jayaram Parliker, VIIIth Eddition, University Press

(2009) Microbiology an Introduction – Tortora, Funke, Case, IXth Edition (2007) Pearson Benjamin

MBM-3012, COMPUTER APPLICATIONS IN AGRICULTURE Objectives : Basic knowledge of computer and its use is an essential aspect of academic learning. The course is designed to provide introductory knowledge to the students so that they can make effective use of computer and internet in their studies and project work.




Unit-I

Introduction to Computers: Characteristics of computers, Generation of computers, classification of computer: Microprocessor, Mini computers, supper computers. Components of a computer system: Central Processing Unit, Input unit, Output unit, Storage Unit. Applications of computer.

Unit-II Hardware/Software: computer memory and storage: Random Access Memory Read only memory, Secondary storage devices, Input/Output devices, Software, Categories of software, Operating system, DOS, Windows.

Unit-III

Computer Networks : Introduction, LAN, MAN, WAN Internet, Transmission media, Guided/ Wired Media, Unguided/Wireless Media, Network Topologies, Bus Topologies, Ring Topology, Star Topology, Mesh Topology, Networking Equipments.

Unit-IV Word Processing: Microsoft Office word (MS Word): Introduction, Working with Word Documents, Creating a new document, opening saving and closing, working with text, Working with Tables, Checking spelling, Adding Graphics, Printing Formatting Text; Applying Font Styles, fonts & point Sizes, setting indents & line breaks, Line & paragraphs spacing, Aligning text, setting Headers & Footer. Suggested Readings :

Computer Fundamental by P.K. Shukla Introduction to Computers by Peter Norton Fundamental of Computers by Rajaraman

MBM-3013, BIODEGRADATION AND BIOREMIDIATION

Objectives :

The proposed course is designed to teach students the scientific principles of microbiological treatment technologies to clean up contaminated environments and to generate valuable resources for the human society. The course will include the fundamentals of Biodegradation, and bioremediation of organic contaminants and toxic metals in soil, water and air.



UNIT-I

Fundamentals of Biodegradation, Factors affecting biodegradation, co-metabolism and biotransformation, Biodegradation of chlorinated aliphatic compounds, Biodegradation of pesticides, Pseudomonas degradation plasmids: TOL plasmid. Toluene (Tol) degradation pathway, Biodegradation of polyhalogenated compounds by recombinant bacteria- Naphthalene (Nah) degradation pathway.

UNIT-II

Bioremediation for Soil Environment: Introduction to Bioremediation, Biochemical and molecular foundations of Bioremediation, Constraints, advantages and applications, Types of bioremediation - Natural (attenuation) and engineered, Environment of Soil microorganisms, Soil organic matter and characteristics, Soil microorganisms association with plants, Bioremediation of Industrial solvents, pesticides and organics. Biotechnologies for ex-situ and in situ remediation of soil.

UNIT-III

Bioremediation for Water Environment: Contaminants in Groundwater, Bioaugmentation and factors affecting bioaugmentation, Ex-situ Decontamination of Groundwater, Land-fill Leachate Biotreatment Technologies, Industrial Wastewater Biotreatment Technologies, Biotreatment of Surface Waters, Trickling Filters and Biological Towers, Rotating Biological Contactors, Granular Media Filters, Fluidized-bed Reactors, Hybrid Biofllm Processes.

UNIT-IV

Bioremediation of Metals: Definition and characteristic of Metals and Metalloids, Metal-plants-microbes interaction; toxicity and tolerance, Microbial biomass as biosorbant, mechanism of biosorption and biosorption technology. hyper-accumulator plants, Metal Signaling in Plants, PGPR and Metal removal/Detoxification, Rhizobium-legume symbiosis as a tool in bioremediation strategies, metal-mycorrhiza interactions, Phytoremediation: Concept and application. Suggested Reading:

Principles and Applications Rittmann, B.E., and McCarty, P.L., McGraw Hill, 2001. Prescott, L. M., Harley, 3. P., and Klein, D. A., Microbiology, Second Edition, Wm. C. Brown Publishers,

Dubuque, Iowa, 1993. Alexander, M.: Biodegradation and Bioremediation Phytoremediation and Rhizoremediation: Theoretical Background (2006) Eds. Martina Mackova, David N.

Dowling, Tomas Macek Handbook of Biormediation by Norris et al.CRC Press, Inc 1994 Envirnmental Biotechnology: Principles and Applications, Moo-Young et al., Kluwer Academic Publisher,

1996.

ABILITY ENHANCEMENT (DC)

MBM-3072, SEMINAR


Objectives : The seminar lecture is delivered by the student on relevant topic of their choice and assessed by the teachers on the developed criteria. The aim is to develop oral skill of the students for presentation of lecture and to defend queries in an open presentation.

OPEN ELECTIVE

PPM-3023, INSECT PEST OF FRUITS AND VEGETABLE CROPS

Objectives : To give knowledge on insect pests problems and their management on economically important fruit and vegetable crops.



UNIT-I

Identification, distribution, host range, nature of damage, biology and management of insect pests of Tropical and subtropical (mange, guava, citrus, litchi, banana papaya, beer, grapevine, peach etc.) and Temperate (Apple, walnut, cherry etc.) fruit crops.

UNIT-II Distribution, host range, nature of damage, biology and management of insect-pests of Winter (Brassica and Solanaceous) and Summer (Cucurbits etc.) vegetables. Suggested Readings :

Butani, D.K. and Jotwani, M.G. (1984). Insect Pests of Vegetables, Periodical Expert Book Agency, New Delhi

Srivastava, R.P. (1977). Mango Insect Pest Management, IBD Co., Lucknow Verma, L.R. Verma, A.K. and Gautam, D.C. (2004). Pest Management in Horticulture Crops, Principles and

Practices, Asiatech Publ, New Delhi Freyer, J.C.F. (1998). Insect Pests of Fruit crops, Academic Press, New York Atwal, A.S. and Dhaliwal, G.S. (2008). Agrcultural Pests of South Asia and Their Management. 6th Ed.

Kalyani Publication, New Delhi

PPM-3091, BIOLOGICAL CONTROL

Objectives : To provide knowledge on different biological control agents of insect pests



UNIT-I

History and scope of biological control in agriculture. Theoretical aspects. Parasitic and predatory groups of insects. Conservation and augmentation.

UNIT-II Entomogenous pathogens: bacteria, viruses, fungi, nematodes etc. and their mechanism of pathogenicity. Weed control through bionic agents. Success trends and resource inventory in Biological Control. Suggesting Readings :

Upadhyay, R.K., Mukherji, K.G. and Rajak, R.L. (1999). IPM System in Agriculture, Vol-I-III, Aditiya Book Pvt. Ltd., New Delhi

De Bach, P. (1964). Biological control of Insect Pests and Weeds, Chapam & Hall, New York Burges, H.D. and Hussey, N.W. (1971). Microbial Control of Insect and Mites. Academic Press, London Saxena, A.B. (2003). Biological Control of Insect Pests, Anmol Publication, New Delhi Huffaker, C.B. and Messenger, P.S. (1976). Acarine Biocontrol Agents- An Illustated Key and Mannual,

champan & Hall, New York

IV-SEMESTER

MBM-4001, METHODS IN APPLIED AND MOLECULAR MICROBIOLOGY

Objectives:

This paper is specifically developed to provide recent updates to the students on the methods and technology used in the field of applied and molecular biology so that the students may get exposure to the state of the art technology used.




Unit-I

Methods for studying microbial biofilm (in vitro and in-situ), detection and characterization of quorum sensing signal molecules, quorum quenching compounds from microbes. Detection and molecular characterization of plant, soil and environmental microbes. Methods of studying Metagenome and microbiome.

Unit-II

Detection, identification and characterization of biologically active compounds (antibiotic enzymes etc.) from microbes and other natural products. Immunodiagnostics for food borne pathogens, green synthesis of nanoparticles by microbes and plants and their characterization.

Unit-III

Principle and applications of colorimetry and spectrophotometry, ultracentrifugation, electron microscopy, ion exchange chromatography, molecular sieve chromatography, Principle and applications of HPLC, atomic Absorption Spectrophotometer, Gas Chromatograph. Agarose Gel electrophoresis, PAGE, Flow cytometry, Fluorescent activated cell sorting (FACS), DNA microarray.

Unit-IV

Isolation of cellular fractions- separation, purification of proteins and amino acids, assay techniques for enzymes, Western, Northern and southern blotting, DNA sequencing, Principle and applications of PCR, RFLP, RAPD, ARDRA, RISA, FISH, AND RECOMBINANT DNA technology. Suggested Readings:

Methods for General and Molecular Microbiology 3rd Edition CA Reddy, ASM Press (2007) Bergey’s manual of Determinative Bacteriology Methods in Applied Soil Biology and Biochemistry K.Alef and Nannipieri P. (1995) AP New York

Molecular cloning by Michael R. Green et. al. Cold Spring Harbor Laboratory Press

MBM-40D1, PROJECT WORK & DISSERTATION

Objectives : This course aims to provide extensive training to the students to develop research synopsis, hypothesis of a problem and to execute experimental plan of work to generate data during in the given period of time. The Students have to compile their project work in the form of dissertation for internal and external evaluation.

M. Marks: 100

Credits: 10

ELECTIVE-II

MBM-4011, MICROBIAL BIORESOURCE & AGRO-NANOTECHNOLOGY Objectives : This course is designed in order to utilize and scientifically manage biodiversity, ranging from surveying and identification, preservation, utilization, conservation and legal management of biological resources. It gives special emphasis to the utilization of microbial biotechnology as a core technology to increase the value of commercial products, such as food and feed, enzyme products, drug and bioactive compounds and biocontrol agents.




Unit-I Fundamental of microbial diversity free living and associated with plants (fungi, bacteria and actinomycetes) present in the forest and agricultural ecosystems and different extreme conditions. Collection, isolation, identification and preservation of microbial cultures for BIOTEC in-house research programmes and for the country’s official depository. Information on the biodiversity, physiology, ecology and host-microbe relationships. Legal and policy studies with the focus on legal management of biological resources and intellectual property management.

Unit-II

Potentials of these microbes and plants and use them for applied purposes such as bioactive and enzyme screening, agricultural and industrial usages, as well as for sustainable community support and natural resource conservation.

Unit-III Bioresources Utilization : discovery of the values to developing microbes and microbial-derived products for various applications. Exploration of microbes and metagenome libraries from niche environments ti identify unique enzymes, and further development of enzymes products for food and feed production and other industrial processes. Activity-guided isolation approach to identify novel bioactive compounds against human and plant pathogens from microorganisms. Microbes for their capability as biocontrol agents against important agricultural pests and their improvement for their efficacies and safety for field applications and to promote sustainable utilization of bioresources.

Unit-IV Introduction to Nanotechnology, Nanoparticles, Categories of nanoparticles, Techniques for characterization of nanoparticles. Natural and artificial synthesis of nanoparticles in microorganisms, Biomimeric and green synthesis of nanoparticles, Nanotoxicology, Applications of nanotechnology in agriculture.

Suggested Readings: Introduction to Nanotechnology by C.P. Poole Jr. and F.J. Owens Wiley Interscience (2003) Biotechnology: Lessons from nature by David S. Goodsell Nanomedicine, Vol. IIA: Biocompatibility by Robert A. Freitas Isolation of Biotechnological Organisms from nature – David P. Labeda, McGraw Hill Publishing co. Biomass and Cell Culturing Techniques – Ramniwas Sharma, Biotech Books. Phytoremediation and Rhizoremediation – Martina Mackova, David N. Dowling and Tomas Series, Springer Biotechnology – Fundamentals and Applications – S.S. Purohit, 4th Edition, Agrobios (India). Basic Laboratory Methods for Biotechnology – Lisa A. Seidman and Cynthiaj J. Moore, Pearson.

MBM-4012, CURRENT TRENDS IN AGRICULTURAL MICROBIOLOGY

Objectives :

This course has been developed with the aim to acquaint and enrich the Masters students with the knowledge on recent developments in Agricultural Microbiology and allied areas, specifically the topics which are not covered through the text books. The course is designed to provide information on the current topics and state of the art techniques used in research.




Unit-I Introduction to nanotechnology, Application of nanomaterials in agri-food system, Nanotoxicology, terminator seed technology, Edible vaccines, Plantibodies, Atomic force microscopy and their applications in microbiology. Microbial biofilm: Agricultural, environmental and medical significance, Plasmid biology: gene dissemination in microbial population.

Unit-II

Recent advances in bioremediation, Phyto remediation and Microbes Assisted bioremediation, Bacterial cell to cell communication (quorum sensing), Microbial polyester, Gene therapy, Biopharming, Bioterrorism, Biofuels, Microbial resource and its application.

Unit-III Effective microbes for extreme environment; stress in microbes and plants; moisture and thermal stress. PGPR formulation and applications, Biofilm based biofertilizer, marine microbes as a source of bioactive compounds, probiotics; characteristic and applications.

Unit-IV Stem cells: fundamentals and applications, gene therapy and its limitations. Green nanotechnology and their application in agriculture. Role of fluorescent protein in conjugative plasmid transfer, uptake of resistant genes. Electronic knows recombinant and edible vaccines. In addition to above topics the course involves a series of lectures by internal faculty and external invited speakers (subject experts) on the recent developments in the field of Agricultural Microbiology. Suggested Readings:

Nanomaterials: toxicity, Health and Environmental issues by Kumar C.S.S.R. Bacterial sinaling 2010, Reinhard Kramer Kristenjung, Wiley Blackwel Publisher Invited lectures notes

MBM-4013, BIOSTATISTICS AND BIOINFORMATICS

Objectives :

Basic knowledge of statistics and bioinformatics and its use are essential aspect of academic learning in the field of Microbiology. The course is designed is provide to introductory knowledge to the students so that they can make effective use of statistical and bioinformatics tools in their studies and project work.




Unit-I Measures of central tendency and dispersion, standard distribution: bionominal distribution and normal curve, Poisson multiple, regression. Test of significance, t, f and Chi square test, Design of experiment, basic principles, completely randomized, block, latin square and split plot design, Principal component analysis (PCA)

Unit-I

Introduction to sequence analysis, Basic of biocontrol data basis, Tools for sequence alignment, Phylogenetic analysis, Gene prediction methods, Visualization and prediction of protein synthesis. Searching literature on pubmed.

Unit-III

Similarity searching by BLAST, Different data bases including gene bank. Sequence formatting, Multiple sequence alignment (e.g. CLUSTALW), Detecting functional sites in DNA; Promoters, exons, PolyA sites. Introducing gene finders, Identification of open reading frames (ORF) and repeats in DNA. Restriction enzyme mapping,

Unit-IV

Internet tools for DNA sequence translation, Prediction of signal peptide, Secondary structure, tertiary structure, transmembrane domains and post-translational modifications including phosphorylation, glycosylation, acetylation, signal peptide cleavage site. Suggested Readings :

Biostatistics,Pn Arora and PK Mulhan, Himalaya Pub. House (2010) Bioinformatics (Secind edition), M.M.Rangs, Agrobios India,(2007) Bioinformatics ( sequence and genome analysis ) by David W. Mount, CBS Publisher and Distributors (2005) Basic Statistical Methods with Application by H.L. Sharma, Agrotech Pub. Academy, Udaipur (2005) Molecular Biology of the Gene” (2000) by J. Watson, N.H. Hopkin, J.W. Roberts, J.P. Stertz,

A.M. Weiner, Freeman Pub., San Francisco. Genes” (VIII) Benjamin Lewin, Oxford University Press, London. Introduction to Bioinformatics” (2002) by S.A. Krawetz and D.D. Womble, Humana Press,

New Jersey, USA.

ABILITY ENHANCEMENT (DC)

MBM-4072, SEMINAR


Objectives: The Seminar lecture is delivered by the student on relevant topic of their choice and assessed by the teachers on developed criteria. The aim is to develop oral skills amongst the student for presentation of lecture and to defend queries in an open presentation.

MBM-4073, FIELD WORK / SELF STUDY

Objectives: The course of field work/self study has been developed for students with the objective to provide field based knowledge of various agricultural practices/ cultivated crop/ pesticide used by the local farmers and problem associated with farmers and preparation of self study report by the student.


