11. Fisheries Microbiology - CIFE Mumbaicife.edu.in/cife/pdf/11. fisheries microbiology.pdf · Journal of Applied and Environmental Microbiology ... means for prevention and prophylaxis

MFSc & PhD Syllabus : Fisheries Microbiology

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M.F.Sc & PhD

Programs in Fisheries

Microbiology -

Syllabus

Indian Council of Agricultural Research

New Delhi


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COURSES

M.F.Sc. (Fisheries Microbiology)

CODE COURSE TITLE CREDITS

MAJOR - CORE COURSES

1. FM 501 General Microbiology 2+1

2. FM 502 Environmental Microbiology 2+1

3. FM 503 Virology 2+1

4. FM 504 Microbial Pathogens of Fish and Shellfish 2+1

MAJOR - OPTIONAL COURSES

1. FM 505 Fish Immunology 1+1

2. FM 506 Fish Mycology 1+1

3. FM 507 Microbial Process in the Environment 1+1

4. FM 508 Microbial Biotechnology 1+1

5. FM 509 Diagnostic Microbiology 1+1

6. FM 510 Microbial Toxins 1+1

7. FM 511 Fermentation Technology 1+1

8. FM 512 Zoonoses and Public Health 1+1

PhD (Fisheries Microbiology)

CODE COURSE TITLE CREDITS


1. FM 601 Advances in Aquatic Microbiology 2+1

2. FM 602 Molecular Techniques in Microbiology 2+1

3. FM 603 Microbial Ecology 2+1

MAJOR - OPTIONAL COURSES

1. FM 604 Bio-active Compounds from Aquatic Organisms 1+1

2. FM 605 Bioremediation 1+1

3. FM 606 Water and Wastewater Microbiology 2+1

4. FM 607 Bioprocess Technology 1+1

5. FM 608 Bioinformatics 1+1

6. FM 609 Advances in Immunology 1+1


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M.F.Sc. (Fisheries Microbiology) SYLLABUS


FM 501 GENERAL MICROBIOLOGY 2+1

Objective To teach the basic concepts in microbiology and the common techniques involved in

isolation and identification of bacterial pathogens.

Theory

Unit I Classification of bacteria and fungi- molecular methods in taxonomy, ribosomal RNA

sequences and evolutionary relationships. Microscopy – bright-field, fluorescence,

phase-contrast, dark ground and electron microscopy. Staining techniques -

chemistry and various types – Sterilization – principles and various physical and

chemical methods.

Unit II Nutritional requirements of microorganisms – general growth media, differential

media, selective media. Isolation, enumeration, preservation and maintenance of

cultures - growth curve.

Unit III Routine tests for identification of bacteria - morphological, cultural, biochemical

and serological. Anaerobic bacteria - methods of anaerobiosis. Basics of mycological

techniques. Introduction to molecular techniques in microbiology.

Practical Microscopic techniques, Micrometry, staining techniques, isolation, enumeration and

identification of microorganisms, serological techniques, culture of anaerobic

bacteria, isolation and identification of fungi, molecular and automated techniques

involved in bacterial identification.

Suggested

Readings

1. Fish pathology by Roberts

2. Microbes in Action: A Laboratory Manual of Microbiology by Harry W.

Seeley, Paul J. Vandemark, and John J. Lee

3. Hawkey P M & Lewis D A - Medical Bacteriology: A Practical Approach,

most recent edition, (IRL Press)

4. Barrow G I & Feltham R K A. - Cowan & Steele’s Manual for the

Identification of Medical Bacteria, most recent edition, (Cambridge University

Press)

5. finfish and shellfish bacteriology manual-Techniques and procedures by

Kimberley A. Whitman

6. Foundation in Microbiology – by Kathleen Park Talaro, Arther Talaro.

7. Introduction to Microbiology – John I. Ingraham, Catherine A. Ingraham A.

Ingraham A. Ingraham, Ronald M; Second edition.

8. Basic and Practical Microbiology – Atlas


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Journals 1. Aquaculture

2. Journal of Fish Diseases

3. Diseases of aquatic organisms

4. Veterinary microbiology

5. Journal of Aquatic Animal Health

Broad

Research

Areas

1. Molecular diagnostic techniques and molecular characterization of pathogens

FM 502 ENVIRONMENTAL MICROBIOLOGY 2+1

Objective To understand the bacterial processes in the aquatic environment with particular

reference to pollution.

Theory

Unit I Microbial communities in the aquatic environment, kinetics of microbial population,

biofilms, microbial interactions – symbiosis, antagonism and commensalisms,

biogeochemical cycles.

Unit II Pollution – nature and types, their effects on living organisms. Water pollution-

microbial changes induced by inorganic and organic pollutants, industrial effluents

and domestic sewage. Water-borne pathogens – faecal contamination; entro-

viruses. Standards for various types of water, conventional wastes and their

treatment – Biological pollution – algal blooms and their effect on fish

production, biological and chemical control of algal bloom.

Unit III Metals as pollutants – accumulation of mercury, cadmium, lead, etc. in fishes,

microbial conversion of mercury. Microbial pollution in industries-corrosion of iron,

acid-mine drainage, cooling systems etc.

Practical Microbial pollution of water, detection and characterization of different indicator

and pathogenic organisms such as S. aureus, E. coli, V. cholerae, Salmonella,

Shigella, etc., by conventional and rapid methods, microbial biofilm formation

and its detection, autotrophic and anaerobic organisms in the environment,

microbial corrosion and fouling, microbial degradation of pollutants, stud y of

hydrocarbon degrading and antibiotic resistant microbes in the environment.

Suggested

Readings

1. Soil Microbiology by Subbarao.

2. Aquatic Microbiology by Rheinheimer

3. Marine Pollution by Clark


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Journals 1. Journal of Applied and Environmental Microbiology

2. General Microbiology

3. Applied Microbiology

4. Hydrobiologia

5. World Journal of Immunology and Biotechnology

Broad

Research

Areas

1. Pollution management

2. Indicator organism

FM 503 VIROLOGY 2+1

Objective To teach the morphology of viruses and their replication strategies with special

reference to fish and shellfish pathogens.

Theory

Unit I Viral morphology, viral taxonomy, mode of viral entry, virus replication strategies,.

Unit II Pathogenesis of important viral diseases of fish and shellfish, viral interference,

cytopathic effect.

Unit III Antiviral agents, viral immunity. General principles of laboratory diagnosis of viral

diseases.

Practical Cell culture; primary culture, passaging and maintenance of cell lines; Isolation of

viruses using cell culture; Purification and characterization of viruses, virus

titration, nucleic acid extraction, quantification of nucleic acid, molecular

identification of viral diseases.

Suggested

Readings

1. Fish diseases and disorders: Vol 3 : viral, bacterial and fungal infections by Woo

and Bruno

2. Fish Pathology by R.J. Roberts

3. Diseases of carps and other cyprinid fishes by D. Hoole, D. Buck, P. Burgess and I.

Welby.

4. Textbook of fish health by George Post.

5. Principle diseases of marine fish and shellfish by Carl J. Sindermann

Journals 1. Journal of fish diseases



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4. Journal of Virological Methods

Broad

Research

Areas

1. Epidemiology of viral disease

2. Rapid diagnostics/ techniques

3. Chemo- and phyto-therapeutic agents

FM 504 MICROBIAL PATHOGENS OF FISH AND SHELLFISH 2+1

Objective The objective of this course is to make aware the students about different

microbial pathogens encountered in closed and open water fisheries and ways and

means for prevention and prophylaxis.

Theory

Unit I Microbial flora of finfish and shellfish, commensals and pathogens; Classification

of diseases; Methods of disease prevention; Detailed stud y of bacteria, viruses

and fungi pathogenic to finfish and shellfish with emphasis on morphology,

epidemiology, pathogenesis, treatment and control;

Unit II Bacterial pathogens: Flavobacterium, Flexibacter, Edwardsiella, Pseudomonas,

Vibrio, Aeromonas, Renibacterium, streptoco ccus, Yersinia, Mycobacteria and

Nocardia. Fungus:Saprolegnia, Apahnomyces, Branchiomyces, Ichthyophonus

Unit III Viral diseases: Lymphocystis virus, Epizootic haematopoietic necrosis virus (EHNV)

and other iridovirus, Herpes virus, aquareovirus, IPNV, Nodavirus, Infectious

salmon anaemia virus, VHSV, IHNV, IPNV, Koiherpesvirus, WSSV, MrNV and XSV,

YHV, TSV, MBV, IHHNV, HPV.

Practical Examination of moribund fish; Sampling techniques for microbiological

investigation; Serological and molecular techniques for disease diagnosis, microbial

identification.

Suggested

Readings

1. Fish disease diagnosis and by Edward C. Noga

2. Textbook of Fish Health by G. Post

3. Fish diseases and disorders by J. F. Leatherland and PKT Wook

4. Environment stress and fish diseases by Gary A. Wedemeyer, Fred P. Meyer and

Lynnwood Smith

5. Diseases of carps and other cyprinid fishes by D. Hoole, D. Buckl, P. Burgess and I.

Welby

6. Fish disease by R. J. Roberts


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M.F.Sc. (Fisheries Microbiology)

OPTIONAL COURSES

7. Molecular diagnosis of Salmm disease by Carey E. Cunningham

8. Health maintenance and principal microbial diseases of cultured fishes by John a.

Plumb

9. Principal diseases of marine fish and shellfish by carl J. Sindermann

10. Bacteria from Fish and Other Aquatic Animals: A Practical Identification Manual

(C abi Publishing) by Nicky B. Buller and John A. Plumb




4. Journal of Virological Methods

Broad

Research

Areas

1. Molecular ch aracterization of patho gens

2. Disease surveillance

FM 505 FISH IMMUNOLOGY 1+1

Objective To understand the defense mechanisms in fish and shellfish.

Theory

Unit I Immune system in fish. Lymphoid tissues and cellular components of the

immune system. Defence mechanisms in fishes against pathogenic

microorganisms – specific and non-specific defences. Mechanisms of disease

production;

Unit II Types of immune response-humoral and cellular and the interaction between the

two, immunological tolerance and memory function, activation and interaction of T

and B lymphocytes. T-cell receptors, immunoglobulins, theories of antibody

production, monoclonal antibodies, antigen-antibody reactions, complement

system

Unit III Major histo compatibility complex. Vaccines for fishes. Techniques of vaccination.

Host response and effect of environmental factors.

Practical Collection, separation and identification of fish leucocytes, study of non-specific


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defence system by lysozyme assay, phagocytic activity, etc., detection of antibody

producing cells, agglutination test, immunogel diffusion, immuno-electrophoretic

techniques, ELISA, fluorescent antibody test, immuno peroxidase test, cell mediated

immunity assessment by macrophage migration inhibition, methods of vaccine

preparation and techniques of fish immunisation, methods for assessment of

efficacy of vaccines.

Suggested

Readings

1. Immunology by Ivan Roitt

2. Fish immune system by Iwama

3. Fish Immunology By P.K.Sahoo, P.Swain and S.Ayyappan

Journals 1. Fish and shellfish immunology

2. Veterinary immunology and immunopathology

3. Journal of Immunological Methods

Broad

Research

Areas

1. Fish immunoglobulins, Immunomodulators, immunogenetics, Crustacean defence

mechanisms.

FM 506 FISH MYCOLOGY 1+1

Objective To study the characteristics of fungal agents causing diseases in fish and shellfish and

their control measures.

Theory

Unit I Fungi and environment; fungal classifications, biology of fungi, slime, mould,

protist fungi (Chytridiomycota, Hypochitriomycota, Oomycota), true fungi

(Zygomicota, Ascomycota, Basidiomycota), imperfect fungi (Deuteromycota), yeasts.

Unit II Spore and its dispersal, applications of fungi in life - Role of fungi in food

processing and aquaculture, the growth of yeasts and molds in fishes – effect of

heat, chilling, freezing and chemical preservatives on common fungi associated with

fishes.

Unit III Mycotoxins - source and conditions affecting their production. Techniques for

isolation and identification of yeasts and molds .

Practical Isolation and identification of aquatic fungi, fungi involved in food spoilage and

diseases, application of fungi, detection of mycotoxins.


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Suggested

Readings

1. Fish diseases and disorders: Vol 3 : viral, bacterial and fungal infections by Woo

and Bruno

2. Fish Pathology by R.J. Roberts

3. Diseases of carps and other cyprinid fishes by D. Hoole, D. Buck, P. Burgess and I.

Welby.

4. Textbook of fish health by George Post.

5. Principle diseases of marine fish and shellfish by Carl J. Sindermann

Journals 1. Journal of Fish Diseases

2. Diseases of Aquatic Organisms

3. Veterinary Microbiology

4. Medical Mycology

Broad

Research

Areas

1. Epidemiology of EUS

2. Characterization of fungi

FM 507 MICROBIAL PROCESS IN THE ENVIRONMENT 1+1

Objective To understand the microbial metabolism associated with cycling of nutrients and

wastes.

Theory

Unit I Introduction to microbes - Cellular life: morphology, structure, macromolecules,

chemistry (cell composition) - Cell function: genetics and biochemical processing

(transport, enzyme function, pathways, regulation).

Unit II Cell function: energetics (flow of energy in the cell, electron acceptors),

reactions - Cell function: growth (cell division, kinetics of growth, form of growth)

and metabolism (kinetics, end products) – Bacterial genetics and genomics.

Unit III Microbial Diversity - Distribution and detection of microbes in the environment;

- Biogeochemical cycling: C, N, S, P, Fe, Hg - Pathogens in the environment and

public health microbiology, Wastewater treatment - Biodegradation,

Biotechnology: industrial, agricultural, energy, nanotechnology.

Practical Study of microbial processes in vitro, enumeration and identification of bacteria

involved in carbon, nitrogen, phosphorus and sulphur cycles , microbial production

and respiration.


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Suggested

Readings

1. Aquatic Microbiology by Rheinheimer

2. Marine Microbiology by ZoBell

Journals 1. World Journal of Microbiology and Biotechnology

2. Hydrobiologia

3. Journal of Environmental and Applied Microbiology

4. Anaerobe

Broad

Research

Areas

1. Identification and characterization of microbes in biodegradation.

FM 508 MICROBIAL BIOTECHNOLOGY 1+1

Objective To teach the structure and function of nucleic acids, gene expression and its

regulation and the application of biotechnology in disease diagnosis.

Theory

Unit I Prokaryotic and eukaryotic genes, gene cloning systems, plasmids and

bacteriophages as cloning vectors, detection of recombinant DNA and clones,

expression vectors, cloning and expression of mammalian genes in bacteria.

Unit II Structure and function of DNA and R NA; Genetic code; Transcription and

translation; Gene organization, regulation and manipulation; Gene expression;

Identification of gene of interest;.

Unit III Restriction enzyme digestion; Recombinant DNA technology; Bacterial and phage

cloning vectors; DNA fingerprinting; DNA microarrays; Ribotyping; PCR, RT-PC R,

Real time PCR, RNA interference. DNA sequencing, in vitro and site directed

mutagenesis, applications of genetic engineering, environmental aspects of

genetically engineered organisms. Fermentation technology.

Practical Molecular characterization of selected microbes by ribotyping; Isolation of

plasmid vectors, modification of DNA, cloning of PCR amplified fragments,

recognition of clones using lacz system, detection of proteins by Western blotting.

PCR, Recombinant DNA technology (microbes as vectors).

Suggested

Readings

1. Basic molecular biology: Essential techniques by P.D. Darbre.

2. Manipulation and expression of recombinant DNA. A laboratory manual by

Varson and Robertson.


11

3. Principles of gene manipulation and genomics by I.B. Primrose and R.M. Twyman.

4. Molecular cloning. A lab oratory manual b y J. Sambrook and D.W. Russell.

5. Gene cloning and DNA analysis. An Introduction by T.A. Brown

Journals 1. Journal of Marine biotechnology

2. Biotechnology

3. Journal of biotechnology

Broad

Research

Areas

1. Cloning, sequencing and expression of virulence genes of pathogens.

FM 509 DIAGNOSTIC MICROBIOLOGY 1+1

Objective To learn the principles and protocols of diagnostic tests used in the diagnosis of fish

diseases.

Theory

Unit I Common bacterial pathogens of fishes. Handling of diseased fish for

bacteriological examination, Withdrawal of blood and materials from internal

organs for bacteriological examination. Diagnosis and infection experiments -

Cultural and biochemical identification procedures. Mycological techniques.

Unit II Culture media for isolation of pathogens, non-selective, enriched, enrichment and

selective media. Inoculation and purification techniques. Staining methods;

Unit III Serology of microbial disease – agglutination precipitation and ELISA methods in

disease diagnosis. Processing tissue samples for virological examination. Techniques

for isolation of viruses. Serological tests for identification of viruses.

Practical Methods for examination and analysing fish for health certification/diagnosis of

disease condition, techniques for sample collection and processing for

bacteriological, mycological and virological agents, methods for isolation of

various bacterial, fungal and viral pathogens by conventional methods, rapid

nucleic acid based methods and serological procedures.

Suggested

Readings

1. Diagnostic Microbiology, 2nd, W.B. Saunders Company, 2000. de la Maza, L.M.,

Pezzlo, M.T., and Baron, E.J.,

2. Color Atlas of Diagnostic Microbiology, 1st, Mosby, 1997

3. Manual of Diagnostic Microbiology By Wadher and Boosreddy

4. Diagnostic Microbiology by Fingold


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Journals 1. Fish and Shellfish Immunology

2. Journal of Fish Diseases

3. Diseases of Aquatic Organisms

4. Journal of Aquatic Animal Health

Broad

Research

Areas

1. Serological and biochemical characterization of microbial pathogens

FM 510 MICROBIAL TOXINS 1+1

Objective To study the characters and methods of detection of toxins associated with microbes.

Theory

Unit I Microorganisms important in food toxicity. Types of toxins-exotoxins, endotoxins and

miscellaneous toxic factors. Factors affecting toxin production in food. Histamine

toxicity, Food-borne diseases – factors influencing their outbreaks. Preventive

measures to control food toxicity and food-borne diseases.

Unit II Methods of toxin and antitoxin production - Types of toxins, methods of

isolation and detection of toxins produced b y various pathogenic bacteria –

Staphylococcus aureus, Clostridium botulinum, Clostridium perfringens, Bacillus

cereus, Vibrio, Salmonella, Eschericha coli, etc.,

Unit III Fungal toxins – aflatoxins, ochratoxins, etc., Red tides, Marine toxins, Shellfish

poisoning.

Practical Methods for detection of endotoxins and exotoxins, purification and

characterisation of endotoxin and exotoxins from different bacteria, biological and

serological methods to study toxin, setting up enzyme linked immunosorbent

assay, dot blot immunmoassay, western blots to study exotoxins, extraction and

detection of aflatoxins and histamines.

Suggested

Readings

1. General Microbiology – Vol. I and Vol. II – Pawar and Diganawala

2. Fundamentals of Microbiolog y – Frobisher et al.

3. Fundamental principles of Bacteriology – A. G. Salle




13


4. Aquatic Toxicology

Broad

Research

Areas

1. Isolation, purification and Characterization of microbial toxins.

FM 511 FERMENTATION TECHNOLOGY 1+1

Objective To learn the properties of various fermentation process and products from

microorganisms such as bacteria, fungi, yeasts, and actinomycetes.

Theory

Unit I Introduction to fermentation: Rate of microbial growth and death. Fermentation

kinetics, mass transfer diffusion, membrane transport, dialysis, nutrient uptake.

Unit II Fermenter design, operation, measurement and control in fermentation. Aeration

and agitation in fermentation: Oxygen requirement, measurement of adsorption

coefficients, bubble aeration, mechanical agitation, correlation between mass-

transfer coefficient and operating variables. Types of fermentation sub-merged/solid

state. Sterilization-air sterilization, media sterilization

Unit III Batch/continuous fermentation, scale up in fermentation. Product recovery.

Biological waste treatment and in-plant sanitation. Principle and use of biosensor.

Production of vitamins, amino acids, organic acids, enzymes and antibiotics, alcohols.

Practical Follow up of bacterial growth in batch culture, Different methods of microbial

cultivation, Mass transfer across membrane, permeability coefficient,

Measurement of B.O.D., Measurement of C.O.D., Fermenter operation and

measurement, Production of starter, bakers yeast culture, production of citric acid,

alcohol, alcoholic beverages, enzymes, amino acids, Visit to effluent treatment plant.

Suggested

Readings

1. Principles of Fermentation Technology by P F STANBURY, A. WHITAKER, and S. Hall

2. Stanburry P.P. and Whitaker, A. Principles of Fermentation Technology.

Pergamon Press, Oxford UK.

3. Steinkraus, K.H. Handbook of Indigenous Fermented Foods. Marcel Dekker, New

York

Journals 1. Journal of Fermentation Technology

2. Journal of Fermentation and Bioengineering

3. Anaerobe


14

Broad

Research

Areas

1. Optimisation of fermentation parameters.

FM 512 ZOONOSES AND PUBLIC HEALTH 1+1

Objective To learn the zoonotic importance of fish pathogens and toxins produced b y aquatic

organisms.

Theory

Unit I Introduction to food-borne diseases – Classification; food-borne infection and

intoxication- microorganisms important in food borne diseases and food toxicity –

economic importance of food - borne illness

Unit II Factors influencing food -borne disease outbreaks – Sources and transmission of

pathogens in foods: human, animal, and environmental reservoirs; cross-

contamination; food associations - Microbial detection and indicator organisms:

approach and techniques; pathogen indicators - bacteria responsible for food borne

infection and intoxication – bacterial toxin and miscellaneous toxic factors – factors

affecting toxin production in foods – fungal toxins, aflatoxin, ochratoxin and other

fungal toxins – factors affectin g fungal toxin production in food – marine toxins PSP,

ASP, NSP, ciguatera poisoning and other marine toxins – histamines and other

bioamines toxicity.

Unit III Zoonoses; zoonoses of different origins – rare, new, and emerging zoonoses,

trematode cestode and nematode zoonoses – food borne viruses – prevention and

control of food toxicity and food-borne diseases - Government Agency and Food

Safety Policy: Government Branches, HACCP, Risk Assessment - New pathogens and

emerging food borne diseases - Current Food Safety Topic: antibiotic resistance.

Practical Isolation and identification of toxin producing microorganisms and other potent

human pathogens in fish and fishery products – detection of toxins using biological and

immunological techniques.

Suggested

Readings

1. Bernard D. Davis, Renato Dulbecco, Herman N. Eisen and Harold S. Ginsberg. 1980.

Microbiology,

2. Harper International Edn

3. Sullia, S.B. and Santharam, S. 1998. General Microbiology. Oxford and IBH

Publishing Co., New Delhi

4. Branen A.L. and Davidson, P.M. 1983. Antimicrobials in Foods. Marcel Dekker, New

York.


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5. Jay J.M. 1986. Modern Food Microbiology. 3rd Edn. VNR, New York.

6. Public Health Laboratory Service- Practical Food Microbiology, most recent edition

(PHLS, London)

7. Eley A R - Microbial Fo od Poisoning, most recent edition, (Chapman & Hall)

8. Hawkey P M & Lewis D A - Medical Bacteriology: A Practical Approach, most

recent edition, (IRL Press)

9. Barrow G I & Feltham R K A. - Cowan & Steele’s Manual for the Identification of

Medical Bacteria, most recent edition, (Cambridge University Press)

Journals 1. Public Health

2. Public Health Forum

Broad

Research

Areas

1. Zoonotic diseases of fish and shellfish .


16

Ph.D. (Fisheries Microbiology) SYLLABUS


FM 601 ADVANCES IN AQUATIC MICROBIOLOGY 2+1

Objective To introduce the students to the recent developments in aquatic microbiology, the

distribution, interactions microbes with each other and with other biota, methods

of study and sampling procedures.

Theory

Unit I Microbial communities in the aquatic environment: distribution; nutrients, oxygen

and pH gradients; open and heterogenous systems; microbial consortia; surface

attachment and biofilm development. Oligotrophy, autotrophy and heterotrophy -

Methods of study Sampling procedures: collection and processing. Detection of

microbial populations: culture-dependent analyses; ELISA; ATP detection; biosensors;

signature chemicals. Direct observation: light microscopy and fluorescence

techniques (FAT, INT, DAPI, acridine orange); ESEM and SEM; Confocal Laser Scanning

Microscopy; Atomic Force Microscopy..

Unit II Activity measurements: enzyme assays; radioisotopes; isotopic fractionation; use of

microelectrodes. Molecular analysis of aquatic communities: signature sequences;

phylogenetic probes and genetic stains; FISH; PCR ; microbial community analyses.

Biodegradation and methanogenesis in aquatic ecosystems. Nanotechnology - The

microbial loop; diversity and exploitation of marine fungi and microalgae.

Unit III Extremophiles: halophilic, pyschrophilic and barophilic bacteria; nutrient cycling at

hydrothermal vents. Thermophilic microbes in hot springs. Food Webs, Bacterial

Energetics, Marine Bacteriophage, Marine Bacteriovors, Symbiosis and Mixotrophy -

Impact of pollution: consequences of eutrophication; toxic blooms; microbial

responses to water pollution by sewage, halocarbons, oil, heavy metals and toxic

waste, including acid mine drainage. Microbial fouling of surf aces - Waste

stabilization ponds; artificial wetlands.

Practical Sampling procedures, Microscopic examination–light, Fluorescence and phase

contrast. Culture of microbes, enzyme assays, molecular detection and

characterization – FISH, PCR, ribotyping, bacterial response to heavy metals and toxic

wastes.

Suggested

Readings

1. Microbial Ecology of the Oceans, David Kirchman,ed. Wiley-liss

2. Freshwater Microbiology: Biodiversity and Dynamic Interactions of

Microorganisms in the Aquatic Environment by David Sigee


17

3. Aquatic Microbiology by Gerhard Rheinheime.

Journals 1. Aquatic Ecosystem Health Management

2. Aquatic Ecosystems

3. Aquatic Living Resources

Broad

Research

Areas

1. Extremophiles, pollution management, biodegradation, optimization of

biogeochemical cycles in managed ecosystems.

FM 602 MOLECULAR TECHNIQUES IN MICROBIOLOGY 2+1

Objective To understand the molecular techniques used in genetic manipulation.

Theory

Unit I Microbial genetics – chemical nature and structure of genetic material; forms of

DNA; Basic concepts- gene, genome, genotype, phenotype; Genetic code – definition

and properties.

Unit II Techniques for isolation of DNA, determination of G+C content, restriction

fragment length polymorphism and significance, isolation and characterisation of

plasmid DNA, plasmids as cloning vectors, gene transfer by conjugation,

transformation, transduction. Gene expression, detection of proteins,

immunoblotting.

Unit III Detection of genes b y polymerase chain reaction, use of gene probes. Non-

radioactive probes for DNA and proteins, molecular epidemiology.

Practical Isolation of DNA and RNA; Quantification of DNA and RNA, gene amplification,

primer designing, gene cloning-restriction digestion, ligation and transformation,

gene sequencing, gene expression, immunoblotting, design and application of gene

probes.

Suggested

Readings

1. Basic molecular biology: Essential techniques b y P.D. Darbre.

2. Manipulation and expression of recombinant DNA. A laboratory manual by

Varson and Robertson.

3. Principles of gene manipulation and genomics by I.B. Primrose and R.M. Twyman.

4. Molecular cloning. A lab oratory manual b y J. Sambrook and D.W. Russell.

5. Gene cloning and DNA analysis. An Introduction by T.A. Brown.


18

Journals 1. Journal of Marine biotechnology

2. Biotechnology

3. Journal of biotechnology

Broad

Research

Areas

1. To identify, clone, sequence novel genes form fish and microbes.

FM 603 MICROBIAL ECOLOGY 2+1

Objective To understand the basic principles and interactions in microbial systems and their

roles in the broader ecology of earth.

Theory

Unit I Introduction: History, Microorganisms and their Environments, Microbial Evolution,

Phylogeny and Taxonomy of Microorganisms, The Chemical Basis of Microbial Life -

Microbial Cell: Prokarya vs. Eukarya - Bioenergetics - Microbial Growth and the

Limiting Factors - Prokaryotic Diversity:

Unit II Eubacteria and Archaea - Prokaryotic Diversity: Cyanobacteria and

Prochlorophytes - Eukaryotic Diversity: Fungi and Protists -Eukaryotic Diversity:

Protists - Sub-cellular Life: Viruses and Plasmids. Microbial Metabolism, Microbial

Diversity, Methods: Numbers, Biomass and Activity, Methods: Molecular and

Genomic, Grazing and the Microbial Loop, Viruses, Dissolved Organic Matter

(DOM), Phytoplankton Taxonomy and Ecology - Microbial Interactions and

Community Structure - Water-Column Microbes and Biofilms - Periphyton

Communities and "Marine Snow" - Sediment Communities and Microbial Mats -

Soil and Lithospheric Communities - Microbial Food Web. Trophic interactions and

flows of material and energy in marine food webs, Geomicrobiology, Climate and

Microbes, Marine Pathogens and Public Health Microbiology.

Practical Identification of bacteria, fungi, algae, protests; periphyton, benthos; estimation

of production, respiration, indicator organisms; estimation of DOM.

Suggested

Readings

1. Atlas and Bartha (1998 ) Microbial Ecology: Fundamentals and Applications. 4th

Edn

2. Fenchel (1987) Ecology of Protozoa: The Biology of Free-livin g Phagotrophic

Protists

3. nd Fenchel (1998) Bacterial Biogeochemistry: The Ecophysiology of Miner al

Cycling. 2nd

Edition


19

Ph.D. (Fisheries Microbiology)

OPTIONAL COURSES

4. Madigan et al. (1999) Brock’s Biology of Microorganisms. 9th

Edn

5. Kemp et al. (1993) Handbook of Methods in Aquatic Microbial Ecology.

Journals 1. Aquatic ecosystems health management

2. Aquatic ecosystem

3. Aquatic living resources

Broad

Research

Areas

1. Community and bacterial metabolism, biofilms and their uses.

FM 604 Bio-active Compounds from Aquatic Organisms 1+1

Objective To realize the potential of aquatic organisms as a source of bio-active compounds.

Theory

Unit I Antibacterial compounds from aquatic sources. Marine toxins – paralytic shellfish

toxins, diarrhetic shellfish toxins, amnesic shellfish toxins, neurotoxic shellfish

poisoning, venerupin shellfish.

Unit II poisoning, ciguatera toxins, tetradotoxins and their origin. Production of

emulsification products, polysaccharides, fatty acids from marine organisms.

Practical Testing antibacterial activity of compounds, assay for marine toxins, detection of

microbial polysaccharides, fatty acids and other bioactive compounds.

Suggested

Readings

1. Natural Compounds as Drugs, Volume I (Progress in Drug Research) by Frank

Petersen and René Amstutz

2. Bioactive Compounds in Foods: Effects of Processing and Storage (Acs

Symposium Series) by Tung-Ching Lee and Chi-Tan g Ho

3. Biologically Active Natural Products: Agrochemicals by Horace G. Cutler

and Stephen J. Cutler

Journals 1. Toxicon

2. Toxicology and applied pharmacology

3. Toxicology


20

Broad

Research

Areas

1. Isolate, identify and characterize various toxins from aquatic organisms.

FM 605 BIOREMEDIATION 1+1

Objective To learn the natural decomposition processes that take place in the environment and

the possible interventions.

Theory

Unit I Concepts of bioremediation, biogeochemical cycles, isolation and screening

bioremediation’s microbes, organic compound contaminants bioremediation, heavy

metal and xenobiotic compounds bioremediation, hydrogen bioremediation, and

engineering techniques used in bioremediation. Application of microbial activities on

petroleum technology. Microbes in waste treatment industries.

Unit II Innovation on exploiting microbes for positive purposes in human living.

Technologies of commercial importance advances in biogas technology - case

study. Concept of rDNA technology - plasmid - cloning of DNA - mutation -

construction of microbial strains. Environmental effects and ethics of microbial

technology - safety of genetically engineered organisms.

Practical Decomposition of model substrates, isolation of active bacteria and fungi,

phytoremediation, preparation of consortia.

Suggested

Readings

1. Schlesinger, W. H. 1997 Biogeochemistry: An Analysis of Global Change. 2nd

Edition, Academic Press, San Diego.

2. Some appropriate journals and sources: Biogeochemistry, Global

Biogeochemical Cycles, Nature, Limnology & Oceanography, Ecosystems, Amb

io, BioScience, SCOPE books (Wiley & Sons, Kluwer, Island Press)

3. Environmental Biotechnology: Principles and Applications, B. E. Rittmann and

P. L. McCarty McGraw Hill, 2001.

4. Brock Biology of Microorganisms, M. T. Madigan and J. M. Martinko, Prentice

Hall, 2005


2. Anaerobe

3. Pollution Research


21

Broad

Research

Areas

1. Bioremediation of pollutants and metabolites, isolation and development of

microbial consortia.

FM 606 WATER AND WASTEWATER MICROBIOLOGY 2+1

Objective To learn the impact of microbes in water quality and use of them for treatment of

wastewater.

Theory

Unit I Introduction to water and waste water microbiology, Microbial growth kinetics,

microbial enzyme kineties; metabotic pathways; Microbial metabolism for waste

and pollutions; Pollutants and their types, nature, sources; Pretreatment and

handling of hazardous wastes, microbiological and biochemical aspects of waste

treatment, characteristics of waste water; aerobic and anaerobic waste water

treatment processes; Activated sludge process; trickling filter; lagooning process;

rotary disc biological contractor, two stage biomethanation process, Biological

treatment of wastes; effluent disposal and reuse; Downstream processing of

biological waste treatment processes.

Unit II Bioconcentration - bioaccumulation - bio-magn ification - bioassay -

biomonitoring.- Microbial degradations and biotransformations: Degradation of

biopolymers: cellulose, xylan, starch and other glucans, pectin, lignin and chitin,

protein, nucleic acids, lipids and fats, and polyhydroxy alk anoates (bioplastics).

Microbial degradation of hydrocarbons: Methane, ethane, propane, butane and

other long chain alkanes, alkenes, alkynes and aromatic compounds. Microbial

degradation of halogenated and sulfonated compounds. Biodegradation of

pesticides.

Practical Media preparation and inoculation - staining - environmental factors - b acteriolo

gical analysis of water, sewage, and test for plate count - coliforms - fecal

coliforms - E.coli - S. fecalis - M.P.N. and M.F. techniques. Techniques for studying

aquatic organisms - identification of phytoplankton and zooplankton - bioassay

study and biodegradation.

Suggested

Readings

1. The microbial world 1990. Stanier, P.R., Ingraham., Wheelis, M. L and Painter,

P.R. Prentice Hall of India Private Limited, New Delhi.

2. Microbiology - Pelzar, Reid and Chan. Tata - Mc Graw Hill Publishing Company

Limited, 1996

3. Microbiology Davis, B.D., Dulbecco, R., Eisen, H.N and Ginsberg,H.S.Harper

and Row Publishers, Singapore.,1992


22


2. Anaerobe

3. Pollution Research

Broad

Research

Areas

1. Biochemical and microbial handling and treatment of wastewater.

2. Bioassays for bioaccumulation and biomagnification

FM 607 BIOPROCESS TECHNOLOGY 1+1

Objective To learn the techniques for bulk processing, production and purification of biologicals.

Theory

Unit I Raw materials for bioprocessing, comparison of chemical and biochemical

processing based on energetics and environmental issues. Development of inocula,

kinetics of enzymatic and microbial processes, optimisation studies, sterilization of

media, air and equipment, modes of cell cultivation, general principles of

bioreactor design and their operation - Downstream processin g, separation and

purification techniques, quality assurance testing, representative examples of

microbial products, vaccines and vaccine development.

Unit II immobilization of cells and enzymes: principles, methodology and applications,

isintegration of cells, separation of solid and liquid phases, isolation and

purification techniques for proteins and other products based on different

physico-chemical properties, eg., precipitation, adsorption, chromatographic

separations, bio-affinity based methods - Principles of bioprocess control,

bioprocess auto mation and application of computers in bioprocessing,

recombinant products with representative examples, biosafety and environmental

monitoring of GEMs, Introduction to patents, Intellectual Property Rights in

Biotechnology.

Practical Downstream processing, separation and purification of compounds, Preparation

of vaccines, Purification of protein and enzymes by precipitation, adsorbtion,

chromatography and bioaffinity based methods.

Suggested

Readings

1. Biofertilizers by Vyas and Vyas

2. Pharmaceutical Microbiolgoy By Hugo and Russell

3. Enzyme Biotechnology By G. Tripathi

4. Biofertilizers by Aruna Sharma


23

5. Industrial Microbiology by Agarwal/Parihar

Journals 1. Toxicology and applied pharmacology

2. Journal of Fermentation and Bioengineering

Broad

Research

Areas

1. Purification and characterization of bioactive compounds for aquatic animals and

microbes.

FM 608 BIOINFORMATICS 1+1

Objective To understand the uses of information technology and computer for the analysis and

documentation of biological information.

Theory

Unit I Introduction to bioinformatics -Definition of bioinformatics, genomics, proteomics,

functional genomics - Computational biology - As an extension of molecular

biology/essential tools of modern biology. Role of Biology, Mathematics, Statistics,

Information technology and Computer Science in Bioinformatics development, role

of internet.

Unit II Nature of biological information – From Central dogma of molecular biology to

Central Paradigm of Bioinformatics, Sequence alignment – basis of and general

principles involved, global/local, tools available like BLAST - Application aspects

of bioinformatics and historical development, Useful things from Internet to

analyze molecular biology information to be used in microbiological fields. Gene

bank, database structure, DNA sequencing analysis, methods for DNA sequence

prediction and protein information, use of man y application programs related to

bioinformatics, biological function of DNA and protein sequences.

Practical DNA sequencing analysis, methods for DNA sequence prediction and protein

information, using Genbank, BLAST analysis, literature search.

Suggested

Readings

1. Bioinformatics : A primer, Narayan P.

2. Text Book of Bioinformatics, Subramanian C.

3. Bioinformatics methods and applications by Rastogi, Mediratta N. I.

Journals 1. Bioinformatics

2. Journal of Biomedical informatics

Broad

Research

Areas

1. In silico analysis of microbial sequences for studying variation.


24

FM 609 ADVANCES IN IMMUNOLOGY 1+1

Objective To learn the recent developments in the field of fish and shellfish immunology.

Theory

Unit I Phylogeny of fish immune system, specific and non specific immunity,

agglutinins, precipitins, C reactive proteins, complement, humoral and cell

mediated immunity, cells and organs of immune system, cytokines, prophylaxis

and treatment of diseases, vaccines, immunostimulants, hybridoma, polyclonal

and monoclonal antibody production, immune tolerance and auto immune

diseases; Invertebrate immunology.

Practical Preparation of antigen, raising of antibodies, separation of immunoglobulins,

agglutination test, agar gel precipitation test, immunodiffusion, chromato-graphy,

preparation of conjugates, ELISA, Dot ELISA, LAT, Western blotting, isolation and

separation of lymphocytes.

Suggested

Readings

1. Immunology by Ivan Riott

2. Fish immune system by Iwama

3. Fish Immunology by P.K. Sahoo, P. Swain and S. Ayyappan

Journals 1. Fish and shellfish immunology

2. Veterinary immunology and immunopathology

Broad

Research

Areas

1. Fish immunoglobulins, Immunomodulators, immunogenetics, crustacean defence

mechanisms

Documents

11. Fisheries Microbiology - CIFE Mumbaicife.edu.in/cife/pdf/11. fisheries microbiology.pdf · Journal of Applied and Environmental Microbiology ... means for prevention and prophylaxis