FST 305 GENERAL MICROBIOLOGY

1. FST 305GENERAL MICROBIOLOGY By Prof. Olusola Oyewole And Dr. OlusegunObadina

2. Know Your Lecturers Prof. Olusola Oyewole Dr. Olusegun Obadina

3. Class organization • Learners Introduction. • Explanation of the Learner- Based learning. • Expectations. • Lectures • Practical • Assessment

4. Course Content • Historical development and scope of microbiology. • Functional classification and morphology of micro-organisms, microbial nomenclature-fungi, algae, bacteria, viruses, protozoa, Rickettsia and cultivation and isolation of micro-organism – • Use of microscopy, culture media, staining methods, maintenance of cultures. • Microbial physiology and biochemistry; reproduction; useful and harmful micro-organisms. • Public health considerations of micro-orgnisms.

5. This Course LECTURES PRACTICALS The theory aspects of the module will be elaborated through relevant laboratory exercises to illustrate the principles and concepts of the subject matter • Basic knowledge of the diversity of microorganisms. These are; bacteria, viruses, protozoa and fungi. Their biology as it relates to their economic importance in the environment are discussed in detail.

6. General Overview. I This Course is a study of organisms that can not be seen with the unaided eye unless with the help of a microscope. They are referred to as microorganisms. More commonly they are called microbes. These are bacteria, viruses, protozoa and fungi. Although viruses are strictly not organisms, they too will be discussed under the same title for convenience. Mycology which is the study of fungi includes some groups like the mushrooms with macroscopic fruiting structures, which appear seasonally above the ground. The study of microbes is called microbiology.

7. General Overview. II The module starts with the history of microbiology; the discovery of microbes and the development of sterile culture techniques, and goes on to explore the diversity of microbes, their major biological characteristics and economic importance. Examples of laboratory exercises meant to familiarise the students with microbiological techniques such as, media preparation, isolation, identification, culture maintenance, growth measurements, staining techniques and preservation are presented

8. What Is Needed To Benefit from the Course • ● Attendance in Lectures – Learner Based Approach • Relevant reference text books. • Students Home assignments and • ● Laboratory equipment such as a microscope, an autoclave, oven, an incubator (various temperatures), Petri plates, materials for bacterial and fungal media preparations, various staining chemicals, identification manuals and other laboratory equipment and materials for standard microbiology work • ● Capacity to facilitate for site visits/field trips.

9. The Learning Plan I.

10. The learning Plan. II

11. The learning Plan. III

12. Module 1 • you will learn about the history of microbiology and appreciate the discoveries of microbes, microscopes and the development of the sterile culture technique. Microorganisms are quite diverse in their distribution, appearance, physiology and metabolism, including their genetics. Bacteriology is a branch of microbiology, which deals with bacteria, which can be classified on the basis of their structure, cellular metabolism or differences in their cellular chemistry. However, classification based on these parameters has limitations in use as a difficulty arises whether the separation of bacteria is between species or between strains of the same species. A more reliable form of bacterial classification uses molecular systematics based on genetic techniques. As a result of this work prokaryotic microbes are taxonomically divided into two groups called Bacteria and Archaea,

13. A Brief History • Early Food Preservation • 900 AD – “Food Poisoning” Recognized • 1795-Appert Developed Canning • 1854-1864-FOOD MICROBIOLOGY BECOMES A SCIENCE • Louis Pasteur

14. Food Preservation Methods Cheese, Beer, Bread, Sauerkraut, Summer Sausage 900 AD Food Poisoning Recognized Emperor Leo VI of Byzantium issued an edict that forbade eating blood sausage prepared by stuffing blood into a pig stomach and preserving it by smoking-BOTULISM Greeks and Romans - 1582 Ergotism, Claviceps purpurea – Rye

15. Food Poisoning was Recurrent because we didn’t know the cause Appert – Food in jars and boiled to preserve, but did not know WHY? 1795 “agents of putrefication” or “fermentable principles” 1854-1864 – Louis Pasteur – discovered scientific basis for preservation methods-FOOD MICRO BECOMES a SCIENCE “pasteurization” – First done in Wine, now milk, juices, etc.

16. Relevant Reading • Alcamo, I. E. 2001. Fundamentals of Microbiology. 6th ed. Menlo Park, • California: Benjemin Cumming. • Fundamentals of Microbiology. Sounders College Publishing, West Washington • Square, Philadelphia, PA 19105. • 2. Frobisher, M., Hinsdill, R.D., Crabtree, K.T. and Goodheart, C.R.1974. • 3. Nester, E.W., Anderson, D.G., Roberts (Jr), C.E., Pearsall, N.N. and Nester, M.T. 2001. Microbiology: A Human Perspective. McGraw-Hill Companies, Inc. • 4. Schopf, J.W. 1999. Cradle of Life: The Discovery of earth’s Earliest Fossils. Princeton University Press, 367 p. • 5. http://www.wikipendia.org/wiki/Microbiology • 6. http://en.wikipendia.org/wiki/Bacteria7. http://gsbs.utmb.edu/bacteria/bacteria.html8. http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookDiversity 2.html9. http://www.wikipendia.org/wiki/Microbiology10. http://www.stlcc.cc.mo.us/fp/users/kkiser/History.page.htm

17. Module 2

18. Module 2 General Objective(s) At the end of this Module, the learner should be able to; • Describe the biology of microbes in terms of their structure and classification, growth and reproduction. • Describe the different techniques in the isolation, identification, and culture of microbes. Specific Learning Objectives • the learner should be able to; • 1. describe how bacteria were discovered. • 2. discuss the development of the culture technique. • 3. classify bacteria based on their characteristics • 4. explain the nutritional requirements of bacteria. • 5. discuss metabolic activities of bacteria. • 6. describe the conditions necessary for optimum growth of bacteria. • 7. explain the genetics of bacteria.8. explain the economic importance of bacteria. • 9. demonstrate the techniques used to isolate and stain bacteria for

19. Microbial Diversitieshttp://en.wikipedia.org/wiki/Bacteria Different Shapes and Sizes The Basic Cell

20. On Plate

21. Bacterial Morphology

22. The Structure of the Bacterial Cell

23. Introduction

24. Lecture • What is Microbiology • Different Branches of Microbiology • Importance of Microorganisms to Man • Microbial Diversities • Microbial Examination • Growth and Different Stages of Growth • Microbial Nutrition and Reproduction

25. Learning Issues • Culture - pure culture and mixed culture. • Morphological shapes of bacteria • The Gram stain technique • Classification of Bacteria • Factors that affect bacterial growth • Phases of microbial growth • Differentiate between: • ● Mesophile and thermophile. • ● Preservation and pasteurisation. • ● Sporulation and germination. • ● Selective medium and differential medium

26. Practicals • Practical skills are mandatory for this Module. • A number of laboratory exercises can be carried out in microbiology. These may include; microscopy, aseptic techniques, bacterial distribution in defferent environments, pure culture techniques using selective media, making a simple smear

27. Practicals • Title: Culture of bacteria and their characteristics • You are required to take samples of water, soil, spoiled food including any such environment of interest. Study the morphological diversity of bacteria using agar plates. Use different staining techniques to identify the gram positive and gram negative bacterial types.

28. Practical Reporting 1. Title: The title should be concise. It is a summary of the body of work that covers the contents of the task under investigation. 2. Introduction: A brief statement of the background to the subject, its importance and justification for the study. 3. Objective(s): A statement of the main expected outcomes (achievements) from the study. 4. Methods: An explanation of the details of how the objectives are going to be achieved. This is important because someone else should be able to use the description of your methods in order to repeat the outcomes of your work 5. Results: Results are better presented in form of pictures tables, graphs, or charts. These should carry a short and clear title, with a description of the results. 6. Discussion: An opportunity is provided for the interpretation of results focusing on the objectives. Comparisons and similarities in the results with other published works are discussed and acknowledged. 7. Conclusions: A statement is made as to whether the objectives of the exercise had been achieved. 8. Recommendations: Suggestions are made about what needs to be investigated further arising from some inconclusive results from the work. 9. References: all references used in the write up should be acknowledged in this part using an accepted international

29. Assignment Write a brief summary of about 100 words on each of the following items: • 1. Discoveries of microbes and microscopes.2. The main features for classification of bacteria3. Selective media for bacteria • 4. Asexual and sexual reproduction in bacteria. • 5. Bacterial Genetics6. The importance of bacteria in the environment, food industry and agriculture

30. Possible Examination Question1. • Write a brief essay (500-800 words) on the importance of bacteria in medicine, agriculture and water quality. • Briefly describe the methods of measuring bacterial growth. • Explain, with the aid of a diagram, a typical bacterial growth curve.

31. Further Reading • http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookDiversity 2.html • ● http://en.wikipendia.org/wiki/Bacteria • ● http://en.wikipedia.org/wiki/Microscopy • ● http://en.wikipedia.org/wiki/Category:Laboratory_techniques • http://en.wikipedia.org/wiki/Category:Microbiology_techniques • http://en.wikipedia.org/wiki/Deer_Island_Waste_Water_Treatment_Plant • ● Frobisher, M., Hinsdill, R. D., Crabtree, K. T. & Goodheart, C. R. 1974. Fundamentals of Microbiology. Nonth Edition. Philadelphia: Saunders College Publishing. • ● Any other Microbiology book

32. Module 3 • Mycology

33. Summary of the Learning Activity This learning activity is going to cover the general characteristics of fungi, mycelial structure and organization, types of nutrition, reproduction, ecology, classification and their economic importance.

34. General Overview. I • The study of fungi called mycology developed as a branch of botany. However, fungi are now considered to have unique characteristics to justify placing them in a separate Kingdom of their own called Myceteae. Over 60 000 species of fungi are known. The fossil record suggests that fungi were present 550 million years ago and may have evolved even earlier. • They range from tiny, single celled organisms invisible to the naked eye such as the yeasts to those that have visible fruiting structures such as the mushrooms. Fungi are classified primarily by the type of spores and fruiting bodies they produce, although molecular biology is beginning to take center stage in their taxonomy. • Many mycologists divide the Kingdom Myceteae (the Fungi) into five main phyla; the Chytridiomycota, Zygomycota (zygospore fungi), Ascomycota (sac fungi) and the Basidiomycota (club fungi). The fifth phylum called Deuteromycota (imperfect fungi) is used by some taxonomists for fungi that apparently reproduce only by asexual spores.

35. General Overview. II • Fungi are a member of a diverse group of eukaryotic organisms that unlike plants and animals obtain food by absorbing nutrients from an external source. The majority of fungi grow on and absorb food from substrates such as soil, wood, decaying organic matter as heterotrophic feeders, while others are obligate parasites subsisting on nutrients derived from living plant and animal tissues. Fungi are multinucleate, meaning that one cell can contain two or more nuclei. They obtain their energy from respiration in a similar way that higher plants and animals do. The outer layer of a fungal cell is a cell wall made of chitin substance, followed by a cell membrane below which is a cytoplasm, which contains all the organelles that are found in an animal cell. Unicellular fungi grow by binary fission whereas the multicellular ones do so by extension growth of the apical hypha. Fungal hyphae are collectively termed mycelium. Mycelia release their secondary metabolites to the environment through the cell membrane. Fungi are so diverse in their mode of reproduction to the extent that some reproduce exclusively by asexual means while others combine the asexual and sexual modes of reproduction. And yet others employ hormones in their sexual reproduction.

36. Specific Learning Objectives for Module 2 - Fungi At the end of this unit, the learner should be able to; 1. classify fungi based on their characteristics. 2. describe the structure of a typical septatehypha of a fungus. 3. discuss the growth pattern of cellular and mycelial fungi. 4. explain the major types of nutrition among the fungi. • illustrate the major types of reproduction systems among the fungi using their lifeCycles. • explain the different modes of nutrition among the fungi. 7. explain the metabolism of carbon in fungi. 8. understand culture preservation techniques. • compare and contrast fungi with bacteria. • explain the economic importance of fungi.

37. Lecture Focus • 1.. Classification and General characteristics of fungi. • 2.. Mycelial structure, organization and growth. • 3. Types of nutrition in fungi (saprophytism, parasitism, symbiosis) • 4. Methods of reproduction (asexual, sexual and parasexual) • 5. Major divisions of fungi, their corresponding life cycles and spore types such as ascospores, basidiospores, zygospores,and oospores. • 6. Collection, culture, preservation and identification methods of fungi. • 7. Economic importance (Diseases in plants and animals; nutritive value (as food), in medicine (antibiotics), fermentation processes (brewing), baking, as decomposers, and research.

38. Fungi and Man

39. Classification of Fungi. I • The term mycology is derived from a Greek word mykewhich means ‘mushroom’, and logos which means ‘study’. Therefore, mycology means literary the study of mushrooms. However, the term is commonly used to refer to the study of a group of organisms called fungi, whose singular is fungus. Fungi were believed to be monophyletic and to be derived from an algal ancestor that lost its ability to photosynthesise. However, over time, with the discovery of molecular techniques in determining relationships between organisms it was discovered that the fungi are made up of a polyphyletic group of organisms that, in some cases, are very distantly related to one another. Therefore, fungi are not grouped together because they are closely related, but rather because they share a combination of characteristics as outlined below. Whittaker (1969) proposed a five Kingdom system which to date is the accepted system of classification of organisms. It puts the fungi in a separate Kingdom of their own called the fifth Kingdom. The Kingdom Myceteae (Fungi) is divided into the Myxomycota, the slime molds and the Eumycota, the true fungi.

40. Classification of Fungi. II The more recent classification system based in part on molecular research is summarised below 1. PhylumChytridiomycota: They produce motile gametes assisted by flagella. Their cell wall composition is mostly chitin. The phylum Chytridiomycota has one class the Chytridiomycetes with the orders; Chytridiales and Blastocladiales. 2. PhylumZygomycota: The Zygomycetes are characterised by the formation of sexual spores called zygospores. They are a result of fertilisation between two haploid nuclei to form a diploid zygote.. Two classes are recognised in this phylum and these are; Trichomycetes and Zygomycetes. The species of a Zygomycete can be determined from the type of zygospore produced. An example of a Zygomycete is the bread mold, Rhizopusnigricans.

41. Classification of Fungi. III 3. PhylumAscomycota: The Ascomycetes are also called the ‘sac fungi’ because their sexual spores, the ascospores, are enclosed in a tube-like sac called an asci. The formation of ascospores is similar to that of zygospores, except that the ascospores formed by meiosis are enclosed in the asci. Neurosporacrassa is an ascomycete mold that is used extensively in studies of genetics. The class Ascomycetes includes the unicellular orders Saccharomycetales and Schizosaccharomycetales, the yeasts. The filamentous Ascomycetes include the orders Eurotiales. 4. PhylumBasidiomycota: The Basidiomycetes are called the ‘club fungi’. Their sexual spores, the basidiospores, are formed on fruiting structures called basidia. The Basidiomycetes include some of the fungi whose aggregation of the hyphae result in the development of fruiting structures that are visible to the naked eye. Such fungi are called mushrooms and fall under the order Agaricales. The group includes the classes Teliomycetes, which comprise the rusts and the Ustomycetes, which embrace the smuts.

42. Classification of Fungi. IV 5. PhylumDeuteromycota: This group of fungi is also called the ‘imperfect fungi’. This is a group of fungi whose sexual stage has not yet been discovered. As the sexual stage of a fungus is discovered the fungus is removed from this group and gets its position in the Ascomycota. 6. Phylum Lichens and Mycorrhizae: These are examples of beneficial associations between two different organisms. In Lichens there is an association between an alga (autotroph) with a fungus (heterotroph). The alga provides the fungus with a carbon source while the fungus provides the alga with nutrients from the substratum. The same applies to the association of fungi with plant roots when they form mycorrhizae. The fungus provides the root system of a plant with mineral nutrients while the fungus gets the carbon source from the plant in return.

43. Structure.I Two structural forms exist among the fungi. One kind is unicellular as represented by the yeast cells. The other form is made up of thread like structures. Individual threads are known as hyphae whosesingular form is hypha. Collectively hyphae are known as mycelium whose plural form is mycelia. The mycelium is the vegetative

44. Structure. II Whether it is a yeast cell or a filamentous fungus consisting of hyphae, fungi are typically made up of a porous outer cell wall made up of chitin, unlike the cell wall of plants that is made up of cellulose. Inner to the cell wall is a cell membrane that is convoluted in places to increase its surface area for exchange of materials. These structures are called lomasomes. The cell membrane encloses the cytoplasm, which suspends the cellular organelles typical of a eukaryotic cell. These are; a membrane bound nucleus, golgi complex, endoplasmic reticula, ribosomes, and vesicles.

45. Structure. III Two types of hyphae are represented by different groups of fungi. The lower fungi typically lack cross walls called septa whose singular is septum. Such hyphae are said to be non-septate and therefore coenocytic because their nuclei are contained in one continuous slug of cytoplasm. The hyphae of higher fungi have septa, which divide the tubular filaments into compartments. However, the septa leave a pore at the centre through which protoplasm can flow. Each compartment of a hypha contains one to two nuclei. Vacuoles are characteristic of the older segments of a hypha.

46. Nutrition. I Fungi are achlorophylous, meaning that they do not contain chlorophyll to be able to make their own food like plants do. Fungi depend on other organisms for their carbon source. Therefore, they are heterotrophic feeders. Heterotrophs can either be saprobes, symbionts or parasites. As saprophytes they obtain their carbon source from the by-products of other organisms or from tissue of dead organisms as organic matter. When they are symbiontsfungi usually live in close association with another dissimilar organism in a mutual beneficial relationship. This kind of relationship is called a mutualistic symbiosis.

47. Nutrition. II Other fungi are parasites in character. These are fungi that derive their nutrition from the protoplasm of another organism called the host. Fungi have a common mode of nutrition, which involves the release of enzymes on to the substratum in the environment. The substrate is digested outside the cell and absorption of the products (monomer forms) take place through the porous cell wall and the selectively permeable membrane for eventual assimilation by the cells. Various types of enzymes are produced depending on the type of fungus and the complexity of the substrate. A single enzyme is required to digest for instance a disaccharide, whereas two enzymes will be required to split a molecule of starch to its monomer units and yet three different types of enzymes would be required to digest crystalline cellulose. This kind of digestion which takes place outside the cell is called extracellular digestion. In addition to a carbon source, fungi also need to take in mineral nutrients to supplement their metabolism, just like higher organisms need the supply of nitrogen, potassium, phosphorus, etc.

48. Respiration • Fungi breakdown their carbon sources to release energy for metabolism in the mitochondria like all eukaryotic cells do, through the following metabolic pathways; glycolysis, Krebs cycle and electron transport chain is the main pathway used to release energy for a cell

49. Growth and Development The unicellular fungi grow by binary fission. The mycelial fungi grow by apical extension. The apical compartment has a very thin cell wall at the tip, which allows the apical compartment to extend in length due to internal cytoplasmic turgor pressure. After attaining a maximum volume, the apical compartment under goes nuclear and cytoplasmic division resulting into two compartments.

50. Reproduction In fungi either sexual or asexual reproduction or both may occur by spore production, often produced on specialised structures called conidiophores, which in turn bear conidia or in sporangia, which contain sporangiospores, or variously shaped fruiting bodies such as asci, which carry ascospores, or acervuli on which another kind of conidia are borne. The kinds of reproduction methods are varied according to the type of fungus in reference. However, asexual reproduction is the major means by which fungi reproduce by either fragmentation of cells, binary fission or by budding. The other method of reproduction in fungi is parasexual. Refer to the life cycles of the representative fungi from the different taxonomic groups at the website given in the compulsory readings to appreciate the different kinds of reproductive methods found among the fungi.