Microbes and the Environment

SEMESTER II : MI212
"MICROBES AND THE ENVIRONMENT"

MICROBIAL CLASSIFICATION AND EVOLUTION

Lecture 1: Microbial Classification Systems
Importance of microbial classification systems. Domains of life: Bacteria, Archaea and Eukarya. Hierarchial organisation. Phenotypic Classification: Traditional and standard methods for classification and identification of microbes based on appearance, behaviour and cellular composition.

Lecture 2 & 3: Genotypic and Phylogenetic Classification
Newer approaches to classification and identification of microbes based on genetic characteristics. Understanding and establishing evolutionary relationships between microbes. Small SubUnit RNA as target molecule for phylogenetics and for identification.

Lecture 4-7: Microbial Taxonomy and Nomenclature.
The previous lecture series (Dr. Boyd) has given you an insight into how microorganisms are classified into their various groupings using classical and molecular techniques. Conventionally, bacteria are grouped (systematics) using criteria contained in Bergey?s Manual of Systematic Bacteriology. These tomes (consisting of five volumes) provide the professional microbiologist with the foundations/details of microbial taxonomy. They are far too complex and are perceived as stoical when used as a teaching tool. This series of lectures is designed to give you an insight into the vast diversity of bacteria that are contained in this unique ecosystem called earth. The approach we are going to take is quiet different. Whilst recognisance will be paid to the taxonomic principles contained within Bergey?s manual, we will investigate the characteristics of bacteria under the following headings: (1) Bacteria with industrial applications, (2) Bacteria that are relevant from an environmental perspective, (3) Medically important bacteria and, (4) the Cyanobacteria. The lecture series will mainly be based on chapter twelve of Brock and details will be provided throughout the course of the lecture series on how possible questions should be attempted in the summer examination.

VIROLOGY

Lectures 8 to 14 - Animal Viruses
The composition, morphology and classification of animal viruses. The life cycle of typical animal viruses. Viral disease of Man and animals (including influenza, measles, chickenpox, smallpox, German measles, hepatitis, herpes, rabies, myxomatosis, etc.). Chronic viral infections. "Slow" viruses and prions. Viruses and cancer.

BIOGEOCHEMISTRY & MICROBIAL WASTE TREATMENT SYSTEMS

Lectures 15 and 16:
The microbial planet. Ecosystems and habitats. What roles do microbes play in the environment? Introduction to microbial ecology.

Lecture 17:
Biogeochemistry and biogeochemical cycles ? how do they drive the biosphere? The role of microorganisms in primary production and decomposition.

Lectures 18 & 19 - Biogeochemical cycling of Carbon, Nitrogen & Phosphorus (1).
The biological Carbon cycle in terrestrial and aquatic ecosystems. The impact of humans on the carbon cycle ? global warming.

Lectures 20 & 21 - Biogeochemical cycling of Carbon, Nitrogen & Phosphorus (2).
LECTURER: Dr. Vincent O?Flaherty
LECTURE DATE: February 27th & 28th
The biological nitrogen and phosphorus cycles. Primary microorganisms involved. Environmental consequences of these cycles.

Lectures 22 & 23 - Waste and wastewater treatment (1).
Waste treatment - why? Objectives of waste treatment: 1. To destroy/improve organic compounds in waste materials. 2. To destroy pathogens. 3. Biotransformation to maintain environmental quality.

Lecture 24 - Waste and wastewater treatment (2).
LECTURER: Dr. Vincent O?Flaherty
LECTURE DATE: March 6th
Aerobic and anaerobic wastewater treatment systems and biology. The role of biofilms in these systems.

MICROBES AND DISEASE

Lecture 25 - 27: ? Pasteur and Koch; the founding fathers of Medical Microbiology.
A historical overview of the roles played Louis Pasteur and Robert Koch in establishing that microorganisms are responsible for decay and disease. Pasteur?s Swan-neck flask experiments and the debunking of the theory of ?Spontaneous generation?. ?Koch?s postulates? in the context of anthrax and tuberculosis.

Lecture 28 ? The commensal microflora of man.
The normal (commensal) flora of humans. Factors affecting the profile of microorganisms found on host surfaces. Examination of the microflora found at different anatomical locations including, skin, upper and lower respiratory tract, eye (conjunctiva), gastrointestinal tract and the urogenital tract. Highlight members of the normal flora that are known pathogens.

Lecture 29 ? Host defence against invading microorganisms: The immune system.
The human immune system. Specific and non-specific defence mechanisms against microorganisms. Phagocytosis. Anitibodies and antigens. The structures and roles of the different classes of antibodies. The complement system. Primary versus secondary immune responses.

Lecture 30 ? Anthrax and Bio-terrorism
A historical overview of bio-terrorism. Routes of infection by Bacillus anthracis and clinical manifestations of anthrax. Practical implications of using B. anthracis as an agent of biological warfare.

Lectures 31 ? GI infections: Escherichia coli.
Commensal versus pathogenic E. coli strains. How E. coli strains are characterised by serotype. Enteropathogenic E. coli (EPEC), Enterotoxigenic E. coli (ETEC) and Enterohemorrhagic E. coli (EHEC). Symptoms and prevention of infection.

Lectures 32 - Helicobacter pylori and ulcers.
Recent discovery of the causative agent of stomach ulcers in humans: Helicobacter pylori and Koch?s postulates. Clinical symptoms of infection with H. pylori. Strategies used by H. pylori to survive in the human stomach. Detection and treatment of the disease.

Lecture 33 ? Summary and exam tips.
Summary and conclusion of the ?Microbes and disease? lectures. Advice on how to approach the end of year written exam in Microbiology. Course feedback questionnaires.