ARS/ NET Agricultural Microbiology Syllabus

Unit 1: History of Microbial World

History, development and scope of microbiology, evolution of microbial life. Theory of spontaneous generation. Prokaryotes, archaebacteria and eukaryotes. Techniques used in identification and classification of bacteria. Important groups of prokaryotes include photosynthetic bacteria, chemoautotrophic bacteria, spore-forming bacteria, actinomycetes, heterotrophic bacteria, nitrobacteria, nitrogen-fixing bacteria, cyanobacteria, lactic acid bacteria, halophiles, thermophiles, acidophiles and methanogens. Structure and classification of viruses, bacteriophages, cyanophages, mycophages. Growth of viruses including lytic and lysogenic cycles. Plant viruses, viroids, prions and mycoplasma.

Unit 2: Microbial Ecology and Physiology

Principles of microbial ecology. Microbiology of ecosystems such as soil, rhizosphere, rhizoplane, endorhizoaphere, phyllosphere, fresh and marine water, and air. Microbial interactions including symbiosis, synergism, commensalism, parasitism, amensalism, antagonism and predation. Adaptation of microorganisms to various ecosystems. Microbial growth curve with mathematical expressions of growth in continuous and batch cultures. Diauxic and synchronous growth. Microbial nutrition. Bacterial metabolism including aerobic and anaerobic respiration, electron transport chain, metabolic pathways, microbial photosynthesis, oxidative and substrate level photophosphorylation, metabolism of xenobiotics, metabolism of C1 compounds. Biosynthesis of cell wall, proteins, macromolecules (DNA/RNA) by microbes. Molecular microbial ecology including numerical and molecular taxonomy and identification.

Unit 3: Soil Microbiology

Soil microorganisms: major groups, decomposition of organic matter, and soil health. Root exudates (rhizodeposition) and rhizosphere effects. Exploration of rhizosphere microflora for plant productivity. Microbial biomass. Nitrogen cycle including ammonification, nitrification and denitrification. Biological nitrogen fixation: symbiotic, associative and asymbiotic. Biochemistry and genetics of nitrogen fixation. Microbial transformations of phosphorus, potassium, sulfur and other minor nutrients. Role of biofertilizers in agriculture and forestry. Bioremediation of problematic soils. Plant growth promoting rhizobacteria and their mode of action. Mycorrhiza and their associations. Formation and composition of soil organic matter: ferulic acid, fulvic acid and humic acid.

Unit 4: Environmental Microbiology and Basic Microbiological Techniques

Isolation and preservation of different types of microorganisms. Methods of sterilization and disinfection. Microscopy techniques: optical, bright field, phase contrast, fluorescent, dark field and electron microscopy. Microbial assay of vitamins, enzymes and antibiotics. Pollution of soil, water and air. Role of microorganisms in pollution remediation and amelioration. Sources of pollution and their environmental impact. Microbiology of sewage and industrial effluents and their safe disposal. Management of solid and liquid organic wastes including composting, biogas production, water purification, sewage treatment. Waterborne diseases and effluent management.

Unit 5: Microbial Biotechnology

Industrial production of metabolites such as organic acids, alcohols, and antibiotics. Fermenter designs and types. Control of fermentation processes including batch, feed batch and continuous. Downstream processing in the fermentation industry. Production of single cell proteins, probiotics, hormones, biofertilizers and biopesticides. Phytoremediation. Microbiology of raw and processed foods. Fermented foods including vinegar, wine, sauerkraut, pickles, cheese, and yogurt. Food preservation, contamination and spoilage. Food-borne illness and intoxication. Food as a substrate for microorganisms. Microflora of meat, fish, egg, fruits, vegetables, juices, flour and canned foods. Biodegrading microbes, single cell proteins for use as food and feed, bioactive food and probiotics.

Unit 6: Microbial Genetics, Genomics and GMOs

Genetic mechanisms in microorganisms including bacteria, archaea and viruses. Principles of genetic variation, gene expression and genetic engineering techniques used in microbiology. Basic concepts of genetics: DNA, RNA, and proteins. Types of genetic mutations. Mechanisms of genetic variation. Methods of detecting and analyzing mutations. Transcription and translation in prokaryotes. Regulation of gene expression including operon model and other regulatory mechanisms. Horizontal gene transfer. Bacteriophages and genetic exchange. Plasmids and mobile genetic elements. Genomic analysis and bioinformatics. DNA extraction and purification. Polymerase chain reaction (PCR). Gel electrophoresis and DNA sequencing. Transformation and cloning experiments. CRISPR and gene/genome editing. Genetically modified microorganisms.