BTE 2440 (Intro. Micro.) Sem. I. 2011/12 Instructor Prof. Dr.

. Mohamed Ismail Abdul Karim Tel: 603-6196-4573 E-mail: akismail @iiu.edu.my

Office hours Rm. E5-212.7 Lecture period: Mon. 2.00 pm 3.20 pm Wed. 2.00 pm 3.20 pm

Room: ENG-LRM (E2.3.8) Sem. I 2011/12.

Welcome to BTE 2440 Introductory Microbiology: Types of Microorganisms.

T4 phage -Virus
Cyanobacteria:Partnership between fungi and algae (has green pigment/involve in phytosynthesis). E.g. Blue green algae and bacteria

Fungal wood degrader

Mushroom

Algae Cocconeis pediculus

Protozoa Entamoeba histolytica

Other Category of Microbes found:

Parasitic worm division of eucaryokes

Lichens/Fungi

Main Category of Microoganisms: Bacteria , Yeasts and Fungi found abundant in the environment.

Parasitic worm e.g. tapeworms, nematodes Parasitic worms or helminths are a division of eukaroytic parasitesl that live inside their host. They are worm-like organisms that live and feed off living hosts, receiving nourishment and protection while disrupting their hosts' nutrient absorption, causing weakness and disease. Those that live inside the digestive tract are called intestinal parasites. They can live inside humans as well as other animals. Helminthology is the study of parasitic worms and their effect on their hosts. Diseases caused in humans by helminth infection include ascariasis, dracunculiasis, elephantiasis, hookworm, lymphatic filariasis, onchocerciasis, schistosomiasis, and trichuriasis.

Hookworms attached to the intestinal mucosa

Lichens/Fungi
A lichen is not a single organism, but the result of a partnership (mutualistic symbiosis) between a fungus and an alga or cyanobacteria. The algal and/or cyanobacterial partner(s) possess the green pigment chlorophyll, enabling them to use sunlights energy to make their own food from water and carbon dioxide through photosynthesis.
The thallus, or lichen body, comes in four shapes: Foliose: flat leaf-like lichens. Crustose: crust-like lichens that may be buried in tree bark, or even between the crystals of rocks. Fruticose: miniature shrub-like lichens.one lichen of this type is the famous "reindeer moss" of Lapland. Squamulose: scaly lichens made of numerous small rounded lobes, intermediate between foliose and crustose lichens.

Foliose

Crustose

Fruticose

Squamulose

Course Outline
Introduction to the biology of bacteria, eukarya (big cell) and archaea (resistant to extreme conditions), and prokaryotes organisms (small cell). Topics include stress on: Microbial history, classification, diversity, systematics Microbial nutrition, growth & control Microbial metabolism & genetics Microbial ecology & symbiosis Industrial and applied microbiology

Course Objectives
Significant roles of microorganisms in nature and industry Basic knowledge of microbiology - Biological Applications - Industrial and Engineering applications - Human diseases Foundation for further courses and research and development in biological and biotechnology engineering

Biotechnology Industry
Traditional biotechnology started with the fermentation industry many food products are made from microorganisms. Some application are found in the agricultural and environmental industry bio-control agent, increase soil fertility, nitrogen fixation, carbon recycling, environmental pollution control. Modern biotechnology discovery of DNA (Watson and Creek, 1953) and cloning of Dolly sheep DNA recombinant technology, human genome project, etc . breakthrough in genetic engineering revolutionize the biotechnology industry especially with use of microorganisms for the production of goods and services becomes a reality. Many biochemical and biotechnology products are produced through fermentation. Recombinant Technology- become evident and play major role in biotechnology, transfer of genes between cells become evident here.

Biotechnology Engineering
Application of engineering principles, design and application of bioreactor in scaling up operation in biotechnology industry becomes important in the new century globally. Fermentation and bioprocess engineering in the manufacture of industrial and pharmaceutical products are evident now. Application in food, bioenvironmental and biomolecular engineering becomes important too. Upstream and Downstream processing.

Evaluation method
Mid-term examination Materials week 1-7 Quizzes 3% each quiz. Final examination TOTAL 40% 15% (5/6 total)

45% 100%

Texts
Required Prescott, L.M., Harley, J.P., and Klein, D.A. 2008. Microbiology (7th. Ed.). Mc Graw Hill. Now 8th Edition available (2010).

Recommended 1. Madigan, M.T., Martinko, J.M., and Parker, J. 2000. Brock Biology of Microorganism (9th. Ed.) Prentice Hall. 2. Talaro, K.P. and Talaro, A. 2002. Foundations in Microbiology: Basic Principles (4th. ed.) Mc Graw Hill.
3. Tortora, C.J. 2000. Lab Experiments in Microbiology. Benjamin Cummings Pub.

Biology?
Greek Bios = life + Logos = reckoning What is Biology? Study of life What is life for a biologist? Life is a combination of all characteristics common to all living things and absent from non living things Site where life exists is cell Cell is the simplest small functioning unit of life

Characteristics of living things microbial cell.

Respiration-gaseous exchange, aerobic, anerobic. Nutrition-inorganic and organic nutrients Metabolism-anabolism, catabolism Excretion-waste product transport Sensitivity-stimulus, receptor, effector affected by surrounding environment. Locomotion-movement. Reproduction-sexual and asexual Growth-development

Microbial metabolites

Hallmarks of Cellular Life

Microbes Good guys vs. bad guys?

Bacillus anthracis

Lactobacillus

Neiserria gonorhrrea

Escherichia coli

Microbiology?
Micro (Greek mikros) = small Organism = living body Science or biology of microscopic organisms (very small, unicellular, multicellular organisms) too small to be seen with our naked eye. The discipline is just over a century old (relatively new) Foundation for Molecular biology and Biotechnology

Microbial History
Major events and figures: Antoni Van Leeuwenhoek layu-wen-hook(Dutch)discovered first powerful microscope observed living cells (living algae) difficult to be seen by our naked eye. Louis Pasteur Dispelled Spontaneous generation theory (Decayed matter could produce living matter). He disapprove this theory. Cell need nutrients to grow. Cannot grow automatically on decayed matter alone. Robert Koch (German) Kochs postulate disease caused by germs. Joseph Lister introduce antiseptic agent. Sterilize surface of humans with antiseptic agent can kill microbes.

Antoni Van Leeuwenhoek:

(discover use of microscope to see microorganisms/green algae) Prior, Robert Hooke (England) described fruiting structure of molds in 1664 utilizing compound microscope. (Eukaryote-bigger size) Size enlargement 20-30 times Jan Swammerdam (Dutch) worked on compound microscope. Various technical difficulties Wrote illustrated book Micrographia which inspired Leeuwenhoek

Compound light microscope

Dutch amateur builder, Leeuwenhoek- saw prokaryotessmaller size in 1684. Discovered first bacteria (Green algae) Made over 500 microscopesessentially magnifying glass Excellent lenses grinding, acute eyesight and lighting adjustmentenlargement 200 times Could only view microbes but no techniques available to study them until later in 19th century.

Spontaneous generation theory

Originated from Roman up to Middle Ages Life form spontaneously arose from non-living matter (decayed materials) e.g. microbial cell do live on decayed organic/non organic matter but will grow if expose to water/availability of nutrients. Eg. 1. Mixture of hay and water will produce microbes after few days incubation. Eg. 2. Dust carry microbes. Media in petri dish if expose to air, can support growth of microbes.

Louis Pasteur (French)

Co-founder of modern bacteriology Dispelled Spontaneous generation theory- does not grow automatically but cell need nutrients and does not grow or remain dormant if without nutrients. Pasteurs work with Pasteur flask Sterilization technique Pasteurization Heat liquid (wine) 55OC for few minutes, kill spoilage microorganisms but not good microbes. Attenuation (weakened virus) of virulent (active) microbes Vaccination development for anthrax, fowl cholera, rabbies Discovered indirectly rabbies virus-agent so small cannot be seen under microscope

Industrial Microbiology and Microbial Ecology

Louis Pasteur
demonstrated that alcohol fermentations and other fermentations were the result of microbial activity. Yeasts is involved here. developed the process of pasteurization to preserve wine during storage

Copyright The McGraw-Hill

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Redis experiment proved contamination cause microbial growth.

1668 Francesco Redi-proposed maggots develop from eggs laid by flies contamination must take place here. Meat in jars-open, closed, closed with gauze. Maggots developed only in open flask. Utilized control.

1.

2.

3.

Needhams exp.
1745 John Needham conducted definitive exp. Boiled chicken broth in flask

Let it cool (being exposed before being sealed) Sealed flask.

Microbes grew Concluded that exp. did not support (dispelled) spontaneous generation theory show presence of nutrients support growth of microbial cells..

Spallanzanis exp. proved besides nutrients bacteria needs air too.

Lazzaro Spallanzani-suggested microbes entered from air after boiling media but before sealing the flask. Flask 1 was left open Flask 2 was sealed Flask 3 was boiled and then left open Flask 4 was boiled and then sealed Place broth in flask, boiled, drew air out, create vacuum, sealed, no microbes grew In case of flask 4. Critics-Spallanzani only proved that spontaneous generation could not occur without air. ( Need air besides nutrients)

1.

2.

3.

4.

Pasteurs exp.
Louis Pasteur-boiled broth in flask, heated the neck of flask, and bend it into swan shape (this draw oxygen out and create vacumn). Left flask and no microbial growth found in broth. Air entered flask but microbes settled in neck of flask, could not entered into broth, found no growth in broth. If allowed the broth to touch with the dust in swans neck of flask, microbes are found to grow in the media).

Pasteurization
Ontario, Canada Pasteurization Regulations for Milk 63 C for not less than 30 min., 72 C for not less than 16 sec., kill spoilage microbes. Can destroy spoilage microbes only. Continuous Pasteurizer

Robert Koch (German)

Co-founder of modern bacteriology Koch works on germ theory of disease. Any disease has a causative agent. - must be infected with the causitive pathogn. Discovered endospore in Bacillus anthracis in sheep blood. Able to be transferred in blood stream

Robert Koch-cont.
Purification of mixed bacterial population must isolate the pure culture. Pioneered usage of solid nutrient media

 Staining techniques with various dyes

Endospore stain - SchaefferFulton endospore stain method (all 100X oil immersion)

Robert Koch-cont.
Steam sterilization technique Sterilization parameter: Autoclave at 121O C at 1.05 kg/cm2 (15 psi) for 30 minutes Sterilization temp. is at 1210C/15psi/15min.- can kill all microorganisms. Commonly use to sterilize all microbial media.

Kochs Postulates
Kochs postulate states: 1. Pathogen presents in all pathogenic infected cases and absent in healthy organism. 2. Suspected pathogen grown in pure culture. 3. Suspected pathogen from pure culture should cause disease in healthy organism. 4. Pathogen should be re-isolated in infected organism and be the same with the original causitive pathogen. 5. Disease is caused by pathogenic organisms has to infect people/animal.

Joseph Lister
Solved hospital disease (operative sepsis)-

open wounds caused by infection of microorganisms.

Postulated that sepsis (wound) caused by

pollen like dust from the air (the dust carry microbes).
Clean and dress wound using carbolic acid

Clean wound with alcohol, can kill microbe too.

Formulated antiseptic method for medical

operation

Immunological Studies
Edward Jenner (ca. 1798)
used a vaccination procedure to protect individuals from smallpox
NOTE: this preceded the work establishing the role of microorganisms in disease. - Smallpox vaccine evolved.

Copyright The McGraw-Hill

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Microbial study need to know:

Need to catogorize type of microbes: Bacteriology, virology, mycology, viruses , etc. Role of microbes: Microbial ecology affecting growth. Its application in Medical, Industrial, Environmental, Food and Agriculture sector. Techniques utilized: characterization/Classification and application using Molecular or microbial genetics is more accurate compared to traditional methods. Purpose of study: Need to understand basic and applied microbiology and its application in engineering.

What are Microbes?

Within 5 Kingdoms, Microbes are categorise into 1,2,3
1. Monera-Eubacteria and Archaebacteria 2. Protista -animal like (protozoa)-Paramecium, Amoeba, -plant like protists (euglenoids, diatoms) 3. Fungi: unicellular-yeast, multicellular-mushroom (spores spread by wind, etc.

4. Animalia-Coelenterates, Flatworms, Molluscs, Annelids, Arthropods, Echinoderms, Chordates 5. Plantae Brown algae & red algae, green algae, mosses, liverworts, vascular plants. Note: 1,2,3 difficult to see with our naked eyes.
** Robert Whittakers five-kingdom scheme proposed based on physical structure & metabolic properties (visual-phenotype) in 1959.

What are Microbes?-cont.

Universal tree

** Carl Woeses domains proposed based on genetic material similarity representing evolutionary line in 1990.

Phylogenic tree
Base on evolutionary development of microbes. Determination of their 16s RNA and G+C content of cell Genus and sp. relationship can be determine (able to group them here). Grouping of their closeness and relationship can be drawn then. Many new species can then be evolved if mutation occurs and also if new discovery are found.

Domain-detail branches

Prokaryotes are evolutionarily ancient, for billions of years the only form of life. Prokaryotes were the first type of cell to evolve, and unlike eukaryotic cells, still lack a membrane bound nucleus. Their genetic material is naked within the cytoplasm, ribosomes their only type of organelle.
Prokaryotes are most always single-celled, except when they exist in colonies. These ancestral cells, now represented by members of the domains Archaea and Eubacteria, reproduce by means of binary fission, duplicating their genetic material and then essentially splitting to form two daughter cells identical to the parent.

Ribosomes protein synthesis.

Ribosome involve in protein synthesis, has mRNA (acting as blue print, transfer genetic information) Procaryotic ribosomes have sedimentation value of 70S. Eucaryotic ribosomes have sedimentation value of 80S.

Taxanomy-cont.
SuperKingdoms: 1.Prokaryote (organisms without membrane bound nuclei) - Monera only 2.Eukaryote (organisms with a separate membrane bound nucleus) - Protista, Fungi, Plantae, Animalia 3. Archae live in extreme conditions (high saline, temp., pressure, pH conditions) (cell wall having long chains of hydrocarbons attached to glycerol rather than fatty acids and connected by ester links), also lack peptidoglycan

Taxanomy-cont.
Superkingdom Kingdom Phylum Class Order Family Genus Species Yeast Eukaryote Mycota Ascomycota Hemiascomyceti dae Endomycetales Saccharomyces Saccharomyces cerevisiae Human Eukaryote Animalia Chordata Mammalia Primate Hominidae Homo sapiens

asexual

Microbial Diversity
Microbial Taxonomy & Phylogeny. Summary- diversity of organisms-best to group similar organisms together. Procaryotic gps. (Archaea, Bacteria/Procaryote) first to be developed, followed by eucaryotes. Found 5 Kingdoms have 3 Classes/Domain.Bacteria,Archae,Eucarya. Classification possible evolutionary relationships (phenetic classification, taxanomy and physiological relationship) resently phylogenetic classification become important- based on comparison of ribosomal RNA structure and chromosome sequence found treelike diagrams called dendrograms.

Cillia and Flagella whip-like appendages in cell that are associted motility of cell. Cillia 5 to 20 ug (microns) in length. Flagella 100 200 ug in length. Golgi apparatus sac-like materials (stack of cisternae) found in cell - helps in development of cell membranes and packaging of cell products.

Prokaryotes
Classification based on cell structure: Small in size-1 to 5 um long Lack of membrane enclosed nucleus Lack of complex internal structures Some differences in mechanisms of replication, transcription, translation, genetic transfer from eukaryotes

Eukaryotes
Classification based on cell structure: Bigger in size-More than 5 um long Possesses membrane enclosed nucleus and internal structures Possesses complex internal structures

There are big differences between eukaryotic and prokaryotic cells, but they do have some things in common: Both have DNA as their genetic material. Both are encased in cell membranes. The membranes of Prokaryotic cells and of some eukaryotic cells are surrounded by a strong cellwall.

Both have a similar basic metabolism (the word metabolism refers to the formation and break down of chemicals in the body).

The major difference is that eukaryotes have a nucleus and prokaryotes do not.

Also, eukaryotic cells contain a wide variety of organelles (tiny "organs" or structures inside the cell) that perform various functions. Some of the most important organelles are mitochondria, chloroplasts, lysosomes and ribosomes
Eukaryotic cells are, on average, ten times as large as prokaryotic cells. Their DNA is more complex and is formed into chromosomes. And their organelles enable them to do more complex jobs.

Mitosis and Meiosis.

Mitosis Mitosis (Asexual reproduction)is the process by which a eukaryotic cell separates the chromosomes in its cell nucleus into two identical sets in two nuclei. Mitosis occurs exclusively in eukaryotic cells, but occurs in different ways in different species. For example, animals undergo an "open" mitosis, where the nuclear envelope breaks down before the chromosomes separate, while fungi such as Aspergillus nidulans and Saccharomyces cerevisiae (yeast) undergo a "closed" mitosis, where chromosomes divide within an intact cell nucleus

Two diploid cells

. Chromosomes is reduce by half (from diploid to haploid state, daughter cell receiving one complete set of chromosomes). Haploid cell which act as gametes may fuse with other cell to form diploid cell.

Meiosis is essential for sexual reproduction and therefore occurs in all eukaryotes (including single-celled organisms) that reproduce sexually. is essential for sexual reproduction and therefore occurs in all eukaryotes (including single-celled organisms) that reproduce sexually.

Homologous Chromosomes

Meiosis I Daughter I

Meiosis II Daughter II

Prokaryotic cells, which lack a nucleus, divide by a process called binary fission. Binary fission, or prokaryotic fission, is the form of asexual reproduction and cell division used by all prokaryotes, some protozoa, and some organelles within eukaryotic organisms. This process results in the reproduction of a living prokaryotic cell by division into two parts which each have the potential to grow to the size of the original cell.