Virus Classification and Introduction PDF

General Botany Prof. Nivien Nafady Botany& Micro Dept., Faculty of Science Assiut Univertsity, Assiut, Egypt  Introduction - Human mind is fond of classifying, grouping and differentiating things. Such classification is also essential for the convenience of man...

General Botany Prof. Nivien Nafady Botany& Micro Dept., Faculty of Science Assiut Univertsity, Assiut, Egypt  Introduction - Human mind is fond of classifying, grouping and differentiating things. Such classification is also essential for the convenience of man’s life. Several attempts have been suggested for classification of animals and plants. - The living organisms and the basis for their classification. Viruses, Viroids, and Prions. Richettsiae and Mycoplasma. Bacteria and Cyanobacteria. Fungi. Algae. Lichens.  Microorganisms Single-celled organisms that are too small to be seen with a microscope. Bacteria are the smallest living organisms Viruses are smaller but are not alive. Microorganisms may be prokaryotic or eukaryotic. Prokaryotic cells have no true nucleus or nuclear membrane. Basis for Classification Structural and functional Whittaker (1969) 5 Kingdoms : Plants, Animals, Fungi, Protists, Monera Phylogenetic Relatedness in nucleic acid sequence 3 Domains : Archea, Bacteria and Eukarya  Classification of The Living Organisms 1- The Oldest System (By A Swedish botanists C. Linnaeus, 1707 ) - The living organisms are divided into plant and animal kingdoms ( which showed some contrasting characters:- i.e. a- Animals move – plants don’t. b- Animals are heterotrophic- plants are autotrophic. c- Animals have a definite size- but plants don’t. d- Animal cell have no cell wall but plant cell have a rigid cell wall. 2- The living organisms are included in three kingdoms (By A German Zoologist, Haeckel, 1866) as follow:- A- Protista Kingdom. B- Plantae kingdom. C- Animalia kingdom This classification was suggested after the invention of the compound microscope by Hooke, an Englishman in 1820, and the microbes began to explored with great enthusiasm. Where to put an organism which has some animal as well as some plant characters (e.g. Euglena). 3- The living organisms are included in four kingdoms (Copeland, 1956):- A- Kingdom Monera (prokaryotic ) B- Protista (Unicellular eukaryotic organisms). C- Kingdom Animalia. D- Kingdom Plantae. 4-The living organisms are included in five kingdoms (By Whittaker, 1969):- A- Kingdom Monera ( Prokaryotic). B- Kingdom Protista (Protozoa & Unicellular algae). C-Kingdom Animalia (Animals) D- Kingdom Plantae (Multicellular algae&Plants) E- Kingdom Mycetae (Fungal kingdom). There are three lines of nutrition namely, - Ingestion : for animal kingdom, - Absorption: for fungal kingdom - Photosynthsesis: for plant kingdom.  Major differences among five kingdoms in the Five Kingdom System of Classification Property Monera Protista Fungi Plantae Animalia Cell type Prokaryotic Eukaryotic Eukaryotic Eukaryotic Eukaryotic Cell Mostly unicellular Cell Multicellular Mostly Cell Mostly organization and Multicellular Multicellular unicellular Cell wall Present in most Present in Present Present absent some: absent in others Nutritional Phototrophic,heterotrophic Heterotrophic Heterotrophic phototrophic Heterotrophic class or chemoautotrophic and phototrophic Mode of Absorptive Absorptive Absorptive Mostly Mostly nutrition or Absorptive ingestive ingestive Motility Motile or non Motile or Nonmotile Mostly Mostly Motile motile nonmotile nonmotile  Viruses (Virology) (virus = Toxin; Acellular) 1- History 2- Definition and general features:. a- Non-cellular infectious agent. Infectious particles that require intact living cells for their replication. b- Cannot reproduce itself; can only be reproduced using a host cell. c- Very small (filtrable agents) and require an electron microscope for visualization. d-Very simple structure comprising nucleic acid (RNA or DNA) within a protein coat with or without an outer lipid envelop. Virion: An intact, infective virus particle which is non-replicating outside a host cell is called virion. 3- Nature of viruses Viruses stand in their characters midway between living organisms and non-living world and known as non-cellular organisms (Non-living and living characters of viruses). The non-living characters are:- a- They could be crystallized b-They do not show any recognizable metabolism away from their host or living cell. The living characters are:- a- Incubation period b- Obligate parasitism c-Electronic mutation d-Enzyme production e-Thermal death point f-Host range (wide, narrow and limited).  Enigma of Viruses Living characteristics of virus Living characteristics of virus Non-living characteristics of Non-living characteristics of virus virus 1- Ability to multiply inside Inability to multiply extra a host plant or animal cellularly cell 2. Ability to cause diseases Absence of any metabolic activity 3. Possession of nucleic Absence of protoplasm acid, protein, enzyme, etc. 4. Ability to undergo Can be crystallized. mutation 4- Size They are very small in size ranging from 5 mu to 300 mu. The size of viruses can be adopted by:- a- Filtration through colloid membranes of certain known pore diameter. b- Centrifugation in high-speed centrifuges. c- Electron microscopy (the most important and widely used). 5- Morphology According to the shape, viruses can be classified into:- a- Spherical b- Rod-shaped c- Cuboid d- Spermatozoid Genetic material (DNA or RNA) and protein coat. Sperm- Like virus Rod-shape (bacteriophage) Polyhedral virus RNA viruses: Influenza 6- Composition of viruses The viruses (virion) consist of a nucleic acid (DNA or RNA but never together) surrounded by protein coat. The protein coat is called capsid. It consists of many subunits, which are similar or occasionally dissimilar, called capsomeres. Protein coat = capsid which composed of several units called capsomers Capsid Capsomer Non-enveloped virus 7-Mechanisms 7- of virus infection Since the viruses are intracellular obligate parasites they interact with the susceptible host. This interaction consists of 5 phases:- a- Adsorption b- Penetration c- Blocking of cell information d- Synthesis of virus components e- Release of the new viruses. Viral Multiplication - Basic Steps 1- Virus attaches to host cell: Specific interactions between viral capsid proteins and cellular surface receptors; tropism of viruses. 2- Whole virus or genetic material enters host. 3- Viral DNA or RNA directs host to make viral genetic material and protein. 4- Viral nucleic acids and proteins are assembled. 5- New viral particles are released from cell. Viruses may be classified in several ways: a- According to the host they infect (Man, plants, animals, Bacteria, insects). 1. Plant viruses including algal viruses-RNA/DNA. 2.Animal viruses including human viruses-DNA/RNA. 3.Fungal viruses (Mycoviruses)-ds RNA. 4.Bacterial viruses (Bacteriophages) including cyanophages-DNA. b-According to the type of tissue they usually attack (this in case of the mammalian viruses only; nerve cells, skin cells, internal organs). c- According to the type of nucleic acid (either DNA or RNA) constituting the virus (Subtypes, Deoxyvira and Ribovira). d- According to the shape/symmetry of capsid e- Presence of lipid envelope.  Bacteriophages (Bacterial viruses) 1- History: Twort (1915) and d’Herelle (1917). 2- Morphology and composition: They look like tadpole in shape, with a head and a tail (fig). The head is either round, oval or polyhedral and the tail is cylindrical, hollow long or short but does not provide the phage with motility. The free end of the tail carries a number of tentacle-like fibers. The head is composed of DNA surrounded by a protein sheath which also covers the tail. Head bacteriophage Polyhedral virus Tail Tail fibers  General Microbiology (PhB-104) Nivien A. Nafady Prof. of Microbiology, Botany and Microbiology Department, Faculty of Science, Assiut University Algae Fungi Bacteria  Definition Bacteria : Is a heterogeneous group of uni-cellular organisms about 1-8 μm in diameter Prokaryotic (has a primitive nucleus): - one chromosome - no nuclear membrane - no mitochondria - no sterols Plasmids: extra piece of DNA. Structures of bacteria Basic Shapes Spherical / round…… Coccus (pl. cocci) Rods cylindrical …… Bacillus (pl. bacilli) Very short Bacilli……Coccobacilli Spirillum – spiral Arrangements among Cocci : Pairs………Diplococci Chains……streptococci Clusters…..Staphylococci In four……Tetrad Palisades…..Corynebacterium…….(The bacilli after cell division bend and therefore arranged in a palisade, fence-like structure) SIZE OF BACTERIA Major structures of bacteria cell wall / appendeges & cytosol Internal structures Haploid…..Circular single stranded chromosome (bacteria genome or DNA) DNA undergoes semi-conservative replication ,bidirectional from a fixed point Ribosomes Distributed throughout the cytoplasm Site of protein synthesis Composed of RNA and protein Organized into 30s and 50s subunits.  Cytoplasm The cytoplasm contains a large number of solute low- and high molecular weight substances, RNA and ribosomes.  The cytoplasm is also frequently used to store reserve substances (glycogen depots, polymerized metaphosphates, lipids).  The Cell Envelope Prokaryotic cells are surrounded by complex envelope layers that differ in composition among the major groups.  It comprises the inner cell membrane and the cell wall.  In Gram- negative bacteria an outer membrane is also included.  Functions :Protect the organisms from hostile environments, such as extreme osmolarity, harsh chemicals, and even antibiotics Cytoplasmic membrane function The major functions of the cytoplasmic membrane are: 1)Selective permeability and transport of solutes. 2)Excretion of hydrolytic exoenzymes (degrade the polymers to subunits small enough to penetrate the cell membrane). 3)Bearing the enzymes and carrier molecules that function in the biosynthesis of DNA, cell wall polymers, and membrane lipids. 4)Bearing the receptors and other proteins of the chemotactic. 5)Electron transport and oxidative phosphorylation in aerobic species. Cell wall Bacteria are cells with rigid cell wall surround cytoplasmic membrane and internal structures. Functions of cell wall: - Rigidity - Shapes bacteria - Protection -Porous / permeable to LMW molecules -Cell division - Antigenic determinants The bacterial cell wall owes its strength to a layer composed of a substance known as murein, mucopeptide, or peptidoglycan (all are synonyms). Chemical Structure of Cell Wall Peptidoglycan layer: is a unique large macromolecule, a polysaccharide, consisting of sugars and amino acids that forms a mesh- like peptidoglycan layer outside the plasma membrane rigid part , mucopeptide composed of alternating strands of N- acetyl muramic acid and N- acetyle glucosamine linked with peptide sub units. Attached to the N-acetylmuramic acid is a oligopeptide chain made of three to five amino acids Structure of cell wall Two groups of cell wall depending on reaction to GRAM STAIN GRAM POSITIVE BACTERIA GRAM NEGATIVE BACTERIA External Structures Protrude from the cell into the environment.: Flagella Pili Fimbriae Capsule Flagella Helical filaments Composed of protein FLAGELLIN. Found in Gram positive & Gram negative bacteria. Distribution: - Peritrichous - Monotrichous - Lophotrichous Arrangement of spherical bacterial cells Monotrichou s Lophotrichous Peritrichous Distribution of flagella on bacteria  Glycocalyx : Is a network of polysaccharides that project from cellular surfaces of bacteria, found just outside the bacterial cell wall. This layer can come in one of two forms: 1-capsule 2-slime layer Capsule The capsule is a well-defined structure of polysaccharide surrounding a bacterial cell and is external to the cell wall (Amorphous material surrounds bacteria). Usually polysaccharide Occasionally protein Function : - Inhibits phagocytosis - acts as Virulence factor in some bacteria by assessing attachment to the surfaces (Plays a role in bacterial adherence).  Lecture 2 Microbial nutrition  Microbial Growth Conditions 1. Macronutrients 2. Micronutrients 3. Growth factors 4. Environmental factors: temperature; pH; Oxygen et al. Nutrient requirements Microorganisms require about ten elements in large quantities, because they are used to construct carbohydrates, lipids, proteins, and nucleic acids. Several other elements are needed in very small amounts and are parts of enzymes and cofactors.  Microbial Nutrition Nutrients: Substances in the environment used by organisms for catabolism and anabolism. 1. Macronutrients: required in large amounts, including: carbon, oxygen, hydrogen, nitrogen, sulfur, phosphorus (Components of carbohydrates, lipids, proteins, and nucleic acids ); potassium, calcium, magnesium and iron (cations and part of enzymes and cofactors). 2. Micronutrients: Microbes require very small amounts of other mineral elements, such as iron, copper, molybdenum, and zinc; these are referred to as trace elements. Most are essential for activity of certain enzymes, usually as cofactors. contaminants in water, glassware, and regular media components often are adequate for growth.  Growth Factors (1)amino acids, (2) purines and pyrimidines, (3) vitamins Amino acids are needed for protein synthesis, purines and pyrimidines for nucleic acid synthesis. Vitamins are small organic molecules that usually make up all or part enzyme cofactors, and only very small amounts are required for growth.  We can classify bacteria according to their requirements into 3 groups: Protrophs: bacteria not required any growth factor. Auxotrophs: mutant bacteria that required some growth factor not needed by the wild type (parent) are referred to as auxotrophs. Fastidious: Organism having complex nutritional requirements and needing many growth factors.  Nutritional Classification According to the ENERGY that use for carbohydrate formation or carbon fixation bacteria can divided into 2 groups: 1. Phototrops: Organisms that use radiant energy (light) are called phototrophs. 2. Chemotrophs: bacteria that use energy released from oxidation of chemical compounds.  Chemoheterotrophs Chemoheterotroph is the term for an organism which derives its energy from chemicals, and needs to consume other organisms in order to live. That means you: your body gets its energy from food, and you must consume other organisms such as plants and animals in order to survive. All organisms must solve two problems in order to survive: they must be able to obtain energy, and they must be able to obtain cellular “building materials” such as proteins, lipids, and carbohydrates. Chemoheterotrophs (Hetreotrophs): Organisms that is unable to use carbon dioxide as sole carbon source and requires one or more organic compounds and divided into three group: i- Saprophytic: An organism living on dead organic matter. ii-Parasitic:An organism that derives its nourishment from a living plant or animal host. A parasite does not necessarily cause disease. iii.Symbiotic: The living together of two organisms and each benefit the other such as bacteria of genus Rhizobium and leguminous plants.  Lecture 3 Bacterial Growth Factors Physical and Environmental Requirements for bacterial Growth a A. The effect of Temperature Bacteria have a minimum, optimum, and maximum temperature for growth and can be divided into 4 groups based on their optimum growth temperature: 1. Psychrophiles (cold-loving), 2. Mesophiles (moderate-temperature-loving), 3. Thermophiles (heat-loving) 4. Extreme thermophiles or hyperthermophiles) B. The Effect of Oxygen bacteria show a great deal of variation in their requirements for gaseous oxygen. Most can be placed in one of the following groups: 1. Obligate aerobes require O2 for growth; they use O2 as a final electron acceptor in aerobic respiration. 2. Obligate anaerobes (occasionally called aerophobes) are organisms that grow only in the absense of oxygen and, in fact, are often inhibited or killed by its presense. They obtain their energy through anaerobic respiration or fermentation or bacterial photosynthesis. 3. Facultative anaerobes (or facultative aerobes) are organisms that can switch between aerobic and anaerobic types of metabolism. Under anaerobic conditions (no O2) they grow by fermentation or anaerobic respiration, but in the presence of O2 they switch to aerobic respiration. 4. Aerotolerant anaerobes are bacteria with an exclusively anaerobic (fermentative) type of metabolism but they are insensitive to the presence of O2. They live by fermentation alone whether or not O2 is present in their Oxygen is lethal to some organisms All organisms produce superoxide ( O2-) Superoxide is toxic to cells (steals electrons) Superoxide must be neutralized Superoxide dismutase O2- + O2- + 2 H+ -------> H2O2 + O2 Hydrogen peroxide is also toxic to cells and it must be neutralized Catalase 2 H2O2 --------> 2 H2O + O2 Obligate Anaerobes lack: Superoxide dismutase ( SOD ) Catalase 1. Nearly all organisms contain the enzyme catalase, which decomposes H2O2. 2. Even though certain aerotolerant bacteria such as the lactic acid bacteria lack catalase, they decompose H2O2 by means of peroxidase enzymes which derive electrons from NADH2 to reduce peroxide to H2O. 3. Obligate anaerobes lack superoxide dismutase and catalase and/or peroxidase, and therefore undergo lethal oxidations by various oxygen radicals when they are exposed to O2. The action of superoxide dismutase, catalase and peroxidase. These enzymes detoxify oxygen radicals that are inevitably generated by living systems in the presence of O2. The distribution of these enzymes in cells determines their ability to exist in the presence of O2 C. The Effect of pH on Growth Microorganisms can be placed in one of the following groups based on their optimum pH requirements: 1. Neutrophiles grow best at a pH range of 5 to 8. 2. Acidophiles grow best at a pH below 5.5. 3. Allaliphiles grow best at a pH above 8.5. Growth rate vs pH for three environmental classes of procaryotes. Most free-living bacteria grow over a pH range of about three units. Note the symmetry of the curves below and above the optimum pH for growth.  Lecture 4 Bacterial Growth Factors Bacterial Reproduction Bacteria replicate by binary fission a process by which one bacterium splits into two )In this method of asexual reproduction, there is a separation of the parent cell into two new daughter cell(. Therefore, bacteria increase their numbers by geometric progression. Geometric progression refers to the population of bacteria doubling every generation time as a result of dividing by binary fission. Bacterial Reproduction Growth of A Bacterial Population (Growth curve) Occurs when bacteria are introduced into favorable environment Refers to an increase in number of bacteria in the population Results from bacteria dividing many times by binary fission Population usually goes through 4 phases Phases of Growth Four Phases 1. Lag Phase 2. Log Phase 3. Stationary Phase 4. Death Phase Bacterial growth curve, showing the 4 phases of growth. Growth is expressed as change in the number viable cells vs time. 1. Lag Phase Lag time is defined as the initial period in the life of a bacterial population when cells are adjusting to a new environment before starting exponential growth. Bacteria are first introduced into an environment or media Bacteria are “checking out” their surroundings cells are very active metabolically During the lag phase cells change very little because the cells do not immediately reproduce in a new medium. 1 hour to several days 2. Log (Logarithmic) phase Sometimes called the logarithmic phase or the exponential phase. Rapid cell growth (exponential growth) Population doubles every generation (is a period characterized by cell doubling). Microbes are sensitive to adverse conditions antibiotics anti-microbial agents 3. Stationary Phase Stationary phase results from a situation in which growth rate and death rate are equal. The number of new cells created is limited by the growth factor and as a result the rate of cell growth matches the rate of cell death. The result is a “smooth,” horizontal linear part of the curve during the stationary phase. Death rate = rate of reproduction Death due to environmental stress lack of nutrients lack of water not enough space Metabolic and toxic wastes Reduced oxygen Change pH 4. Death Phase Death rate > rate of reproduction Due to limiting factors in the environment  Fungi Nivien A. Nafady Prof. of Microbiology Botany and Microbiology Department, Faculty of Science Definitions Mycology Mycologists Mycoses Fungus/Fungi Definitions Mycology: is the branch of biology concerned w of fungi, including their genetic and biochemic their taxonomy and their use. Many fungi are useful in medicine and industry research has led to the development of such a as penicillin. Mycology also has important app dairy, wine, and baking industries and in the pro dyes and inks. Medical mycology is the study of fungus organ cause disease in humans. Definitions Mycologists: Scientist (biologist) who stud specializing in fungi. Mycoses: Infection (diseases) caused by a that invades the tissues, causing superficia subcutaneous, or systemic disease.  Definitions Fungus (plural: Fungi): is any member of the group of eukaryotic organisms that includes microorganis as yeasts and molds, as well as the more familiar m These organisms are classified as a kingdom. Traditionally, some textbooks from the United States Canada used a system of six kingdoms (Animalia, P Protista, Archaea/Archaebacteria, and Bacteria/Eub while textbooks in Great Britain, India, Greece, Brazi countries use five kingdoms only (Animalia, Plantae Protista and Monera). Kingdom is the highest rank used in the biological taxonomy of all org are 6 kingdoms in taxonomy. Every living thing comes under one of these 6 kingdoms. The six king are Eubacteria, Archae, Protista, Fungi, Plantae, and Animalia.  Characteristics of fungi Following are the important characteristics of fungi: 1. Fungi are eukaryotic organisms means they have true nucleus whic membranes. 2. They are non-vascular organisms. They do not have vascular syste Phloem are absent. 3. Fungi have cell walls (plants also have cell walls, but animals have 4. There is no embryonic stage for fungi. 5. There are sexual and asexual spores. Sexual spores are Oospores, Ascospores, Basidiospores, etc. and Asexual spores are Sporangios Aplanospores, Zoospores, Conidia, etc. 6. Depending on the species and conditions both sexual and asexual produced.  Characteristics of fungi 7. Reproduction in fungi is both by sexual and asexual means. 8. Sexual state is referred to as teleomorph, asexual state is referre anamorph. 9. They are typically non-motile although a few (e.g. Chytrids) have phase. 10. Fungi exhibit the phenomenon of alteration of generation. They h haploid and diploid stage. 11.Fungi are achlorophyllous, which means they lack the chlorophyll pigments present in the chloroplasts in plant cells and which are necessary for photosynthesis. Characteristics of fungi 12. The vegetative body of the fungi may be unicellular or composed of mic hyphae. 13. Hyphae can grow and form a network called a mycelium. 14. Yeasts are unicellular fungi that do not produce hyphae. 15. The structure of cell wall is similar to plants but chemically the fungal ce chitin (C8H13O5N)n. Chitin: is a long-chain polymer of N-acetylglucosamine, an amide derivative second most abundant polysaccharide in nature (behind only cellulose), it is of cell walls in fungi. Structure of the chitin molecule, showing two of the N- acetylglucosamine units that repeat to form long chains in β- (1→4)-linkage. Characteristics of fungi 16. The cell membrane of a fungus has a unique sterol and ergosterol. 17. Fungi are heterotrophic organisms. They obtains its food and energy fro substances, plant and animal matters sources as they are not capable their food. 18. Fungi grow best in acidic environment (tolerate acidic pH). 19. Fungi digest the food first and then ingest the food, to accomplish this t produce exoenzymes like Hydrolases, Lyases, Oxidoreductase, Transfe 20. Fungi store their food as glycogen and is also known as animal starch. 21. Biosynthesis of chitin occurs in fungi. 22. Many of the fungi have a small nuclei with repetitive DNA (favoured as systems in the molecular analysis of basic biological phenomena) 23. During mitosis the nuclear envelope is not dissolved.  Characteristics of fungi 24. Nutrition in fungi – they are saprophytes (gets energy from dead , or parasites (lives in a host, attack and kill) or symbionts (mutua 25.Optimum temperature of growth for most saprophytic fungi is 20-3 for parasitic fungi. 26.Growth rate of fungi is slower than that of bacteria. 27.Some fungi are macroscopic and can be seen by naked eyes. Mold examples of macroscopic form of fungi. 28.Some are edible, while others are poisonous. Vegetative structure (Non-reproductive) HYPHAE A hypha is a long, branching, filamentous structure of a fung hyphae are the main mode of vegetative growth, and are col mycelium. A hypha consists of one or more cells surrounded by a tubul most fungi, hyphae are divided into cells by internal cross-wa (singular septum). Septa are usually perforated by pores larg for ribosomes, mitochondria, and sometimes nuclei to flow Tubular shape One continuous cell Filled with cytoplasm & nuclei Multinucleate Hard cell wall of chitin Grow at tips Hyphae Pores S Coenocyti c  Hyphae occurs in three forms: Coenocytic or nonseptate, such hyphae have no septa. Septate with uninucleate cells. Septate with multinucleate cells. Hyphal growth Hyphae grow from their tips. (the wall is rigid a only the tip walls is plastic and stretches) Mycelium = extensive, feeding web of hyphae Mycelia are ecologically active bodies of fung Ecology and Distribution Fungi play a crucial role in the balance of ecosystems. They colonize mos on Earth, preferring dark, moist conditions. Fungi are not obvious in the way large animals or tall trees appear. Yet, lik they are the major decomposers of nature. With their versatile metabolis break down organic matter, which would not otherwise be recycled. However, most members of the Kingdom Fungi grow on the forest floor, w dark and damp environment is rich in decaying debris from plants and an these environments, fungi play a major role as decomposers and recycle it possible for members of the other kingdoms to be supplied with nutrien Nutrition in Fungi Fungi are heterotrophic in nutrition. They are chlorop deficient and hence they cannot manufacture carbo using carbon dioxide, water and sunlight. On the basis of mode of nutrition, fungi are classifie groups: 1- Saprophytes 2- Parasites 3- Symbiosis Saprophytes Saprophytic fungi ob dead and decaying o such as decaying pla These fungi lives on matter or excreta of animal origin. Examples: Mucor, Rh Aspergillus Vegetative hyphae o directly absorb food organic matter. Saprophytic fungi pro (enzymes which acts These enzymes dige organic matter in the simpler compounds absorption by the hy  Parasitic fungi take food from ot animals. The living organism on which the is called host. Parasitic fungi are harmful to the produce different diseases. Parasites The relationship between the hos in pathology is known as parasiti Parasitic fungi are of three types 1- Obligate: (Biotrophs), restricted to 2- Facultative: (Hemibiotroph) colon tissues. 3- Necrotrophs: A parasite kills host of penetration, more dangerous tha  Biotrophs (obligate parasite): Organisms which always obtain thei nature from living tissues on which they complete their life cycle ( powdery mildew). Hemibiotroph: A parasite that will attack living tissues (as biotroph continue to grow and reproduce after the tissue is dead (facultativ saprophyte) Necrotroph: A parasite when it kills host tissues in advance of pen and then lives saprophytically. Facultative parasites: which live as saprophytes but under favourab conditions attack living plants become parasites. Parasites or saprophytes may have the faculty to change their mode Examples of parasitic fungi  Symbiosis Fungi have several mutualist with other organisms. In mut organisms benefit from the r Two common mutualistic rel involving fungi are mycorrhiz  A mycorrhiza is a mutualistic relationship between a fungus and a plant. The fungus grows in or on the plant roots. The fungus benefits from the easy access to food made by the plant. The plant benefits because the fungus puts out mycelia that help absorb water and nutrients. Reproduction Reproduction is the formation of new individuals havin characteristics typical of a species. The fungi reproduce by means of asexual and sexual reproduction. Asexual reproduction is sometimes called somatic or vegetative and it does not involve union of nuclei, sex sex organs. The union of the two nuclei characterizes sexual repro  A- Asexual reproduction (somatic or vegetative reproduction ) 1. Budding 2. Fragmentation 3. Fission 4. Sporulation (production of spores) 1- Budding The parent cell produces one or more projections called buds, which later develop necessary structures and separated to grow into new individuals. The parent cell puts out initially a small outgrowth called bud, which increases in size and nucleus divides, one daughter nucleus accompanied by a portion of cytoplasm migrates into bud and the other nucleus remains in the parent cell. Later, the bud increases in size and a constriction is formed at the base of bud, cutting off completely from parent cell. Budding is common in unicellular forms like yeast. Ex. Saccharomyces cerevisiae 2- Fragmentation It is the most common method. Hypha of the fungus breaks into small pieces, each broken piece is called a fragment, which function as a propagating unit and grows into a new mycelium. The spores produced by fragmentation are called arthrospores. 3-Fission In this process, the parent cell splits into two equal halves by the formation of a transverse septum, each of which develop into a new individual. Fission is also common in yeast. 4- Asexual spores The process of production of spores is called sporulation. Spore: it is a minute, simple propagating unit of the fungi, functioning as a seed but differs from it lacking a preformed embryo that serves in the reproduction of same species. Spore germinate to form exact clones of the Parent. asexual spores are different in color , size, number, shape and the way in which they are borne. There are two main types of spores: A) Sporangiospores B) Conidia  B- Sexual reproduction Sexual reproduction in the fungi consists of three sequential stages: 1. Plasmogamy: The fusion of protoplasm. 2. Karyogamy: The fusion of nucleus. 3. Meiosis: Cell cycle involved with the nuclear division. The diploid chromosomes are pulled apart into two daughter cells, eac a single set of chromosomes (a haploid state). Sexual reproduction in fungi frequently takes place under unfavourable environmental conditions. Based on the mating types, they are classifi types: 1. Homothallic – When both mating types are present in the same myce called self-fertile. 2. Heterothallic – When both mating types are present in two different m  This sexual mode of reproduction in fungi is referred to as teleomorp four types: 1. Ascospores 2. Basidiospores 3. Oospores 4. Zygospores In fungi, as in other organisms, sexual reproduction grea increases variability in a species. In fungi, sexual reprodu often occurs in response to adverse environmental cond  Sexual reproduction in fungi consists of three sequential stages: plasmogamy, karyogamy, and meiosis. 1- Plasmogamy, the fusion of two protoplasts without the fusion oof nuclei(the contents of the two cells), brings together two compatible haploid nuclei in the same cell. This state is followed by karyogamy, where the two nuclei fuse and then undergo meiosis to produce spores. 2-Karyogamy, two nuclei types are present in the same cell, but the nuclei have not yet fused. Karyogamy results in the fusion of these haploid nuclei and the formation of a diploid nucleus (i.e., a nucleus containing two sets of chromosomes, one from each parent). The cell formed by karyogamy is called the zygote. 3-Meiosis (cell division that reduces the chromosome n one set per cell) generally follows and restores the ha phase. The haploid nuclei that result from meiosis are incorporated in spores called meiospore. Schematic phylogeny and classification of the early- diverging fungi and related taxonomic groups principally based on Spatafora et al. (2016). Classification of Fungi The most up-to-date taxonomy comprises the described diversity known true fungi, dividing it into nine major lineages: Opisthospo Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Ascomycota a Basidiomycota.  Classification of Fungi The kingdom Fungi contains five major phyla that were established acco mode of sexual reproduction or using molecular data. Polyphyletic, unre reproduce without a sexual cycle, are placed for convenience in a sixth g “form phylum.” Not all mycologists agree with this scheme. Rapid advan biology and the sequencing of 18S rRNA (a part of RNA) continue to sho different relationships between the various categories of fungi. The five true phyla of fungi are the Chytridiomycota (Chytrids), the Zygo (conjugated fungi), the Ascomycota (sac fungi), the Basidiomycota (club recently described Phylum Glomeromycota. The Deuteromycota is an in unrelated fungi that all share a common character – they use strictly ase Note: “-mycota” is used to designate a phylum while “-mycetes” formally is used informally to refer to all members of the phylum. Phylum: Zygomycota or zygote fungi, is a former division or phylum of the kingdom Fung members are now part of two phyla the Mucoromycota and Zoopag Approximately 1060 species are known. They are mostly terrestrial living in soil or on decaying plant or animal material. Zygomycota are terrestrial fungi with a well-developed, coenocytic, haploid mycelium. The thallus is haploid, and chitin and chitosan a significant constituents of the hyphal cell wall. Asexual reproductio zygomycetes results in nonmotile spores called sporangiospores. spores, or zygospores, are produced when two morphologically sim gametangia of opposite mating types fuse. These fungi are saprop weak pathogens, causing postharvest molds and soft rots. Sporangia of bread mold: Sporangia grow at the end of stalks, whic white fuzz seen on this bread mold, Rhizopus stolonifer. The (b) tip are the spore-containing sporangia. General characters Zygomycota, all true fungi, with cell wall contain chitin. Somatic phase as mycelia, hyphae which are generally coenocy because they lack cross walls of septa. The nuclei are haploid w organism is in the vegetative stage. Gametangial Copulation is a type of sexual reproduction in Zyg general, the gametangia fuse with each other, lose their identity develop into zygospore. Most members of Zygomycota reproduce asexually by producin sporangiospores. General characters Most zygomycota are saprobes, while a few species are para Zygomycota usually reproduce asexually by producing sporan Zygomycota reproduce sexually when environmental conditio unfavourable. To reproduce sexually, two opposing mating strains must fus conjugate, thereby, sharing genetic content and creating zygo The resulting diploid zygospores remain dormant and protect coats until environmental conditions have improved. When conditions become favourable, zygospores undergo me produce haploid spores, which will eventually grow into a new Zygomycete life cycle: Zygomycetes have asexual and sexual life cycles. In the sexual life cycle, plus and minus mating types conjugate to form a zygosporangium. Sexual reproduction starts when conditions become unfavourable. mating strains (type + and type –) must be in close proximity for g (singular: gametangium) from the hyphae to be produced and fuse karyogamy. The developing diploid zygospores have thick coats that protect th desiccation and other hazards. They may remain dormant until env conditions become favourable. When the zygospore germinates, it undergoes meiosis and produc spores, which will, in turn, grow into a new organism. This form of reproduction in fungi is called conjugation (although it differs mar conjugation in bacteria and protists), giving rise to the name “conj Rhizopus stolonifer  Rhizopus stolonifer Rhizopus stolonifer is commonly known as black bread mold. It is a member of Zygomycota and considered the most important species in the genus Rhizopus.[ It is one of the most common fungi in the world and has a global distribution although it is most commonly found in tropical and subtropical regions. It is a common agent of decomposition of stored foods. Like other members of the genus Rhizopus, R. stolonifer grows rapidly, mostly in indoor environments. Rhizopus fungi are characterized by a body of branching mycelia composed of three types of hyphae: stolons, rhizoids, and usually unbranching sporangiophores. The black sporangia at the tips of the sporangiophores are rounded and produce numerous nonmotile multinucleate spores for asexual reproduc tion. Rhizopus can reproduce sexually when two compatible and physiologically distinct mycelia are present. The rapidly growing colonies fade from white to dark as they produce spores and are similar to cotton candy (also called candy floss or fairy floss) in texture. Parts of somatic phase in zygomycota Rhizoid Root-like structure , The benefit of rhizoids to confirm thallus o feed and increase surface area for absorption of nutrients ).fou somatic phase of chytridiomycota (chytrids ) and one of the par Sporangia A fruiting body (asexual unit ) having different shapes and sizes a sexual spores. Sporangiophore A specialized hyphal element that bears the sporangium Columella The swollen, dome-shaped tip of a sporangiophore that extends sporangium under suitable temperature and humidity causing o sporangium to release spores. Stolon Horizontal hyphae growing along the surface of growth medium Black bread mold (Rhizopus It spreads over the surface o food sources (often soft fruit and grapes). It sends hyphae absorb nutrients. In its asexu bulbous black sporangia at t each containing hundreds of most zygomycetes, asexual most common form of repro Reproductive Structures of Zygomycete (Rhizopus) Sporangia (asexual) and Zygospore (sexual) Life Cycle of a Zygomycete: Black Bread Mold (Rhizop Reproduces Asexually and Sexually  Phylum : Ascomycota Its members are commonly known as the sac fungi this name comes from forming sexual spore (ascospore). They are the largest phylum of fungi, with over 64,000 species. Among the Ascomycota are some famous fungi: Saccharomyces cerevisia yeast) the yeast of commerce and foundation of the baking and brewing in Penicillium chrysogenum, producer of penicillin, Morchella esculentum, the morel, and Neurospora crassa, using as a model in genetic studies. There are also some in famous Ascomycota, a few of the worst being: Asp flavus, producer of aflatoxin, the fungal contaminant of nuts and stored gra both a toxin and known natural carcinogen, Candida albicans, cause of thru rash and vaginitis and some species cause powdery mildew on plants like Erysiphae sp. is caused powdery mildew on grasses and Cucurbitaceae pla  Phylum : Acomycota General Characters: Mycelium is septate and branched except in yeasts (unicellular/non- hypha). Complete absence of flagellated cells. Cell wall contain large amount of chitin and less cellulose (Chitinous cell walls). Harmful or parasites causing several disease to plant and human. Saprophytes and may produce useful enzymes and vitamins. Asexual reproduction by conidia, which are produced on a specialized hyphae called conidiophore. Ability of somatic assimilative hypha to fuse with another and to exchange nuclei (anastomosis). Occurrence in their life cycle of a dikaryon (diploid).  General Characters: Sexual reproduction by forming ascospores produce inside sacs are called asci (singular: ascus), most asci are cylindrical, or globose each ascus has 8 ascospores. Most produce multicellular fruiting body – the ascocarp in which the asci and ascospores are formed. Asci usually develop on an inner surface of the ascocarp , a layer called the hymenium or hymenial layer. Ascocarp: specialized hyphae formed by parent fungi during sexual reproduction Characteristics of asci and ascocarp important in classification. Examples of Ascomycota Aspergillus Anamorphic genus – close to 100 species 11 different teleomorphic genera produce Aspergillus conidia on conidiophores, including Eurotium, Emericella. Common fungi found in air, soil, water. Grow on a variety of substrates, in humid climates found growing on clothing, shoes, etc. Important as contaminants of stored grain, species produce aflatoxin Produce characteristic conidiophore Conidia produced by phialides – flask shaped conidiogenous cells. Have a characterisitic foot cell. Penicillium spp. Over 95 species connected to 3 teleomorphic (sexual reproduction) genera – Talaromyces, Eupenicillium, Carpentales Very common in soil, conidia found in air, water, soil Food spoilage – on citrus fruits, jelly, cheeses Produce penicillin and other chemicals industrially P. roqfertii, P. camembertii used to make cheeses Asexual conidiophore – not swollen at tip, no foot cell Phialides arranged in a brushlike manner Yeasts Many species associated with flowers, fruits where hi concentrations of sugar are present Many are facultative anaerobes – aerobic respiration fermentation Widely used in brewing (beer, wine) and baking indust Some used as human & animal food, source of vitami Also include some human pathogens – Candida albic normal flora Thallus is typically unicellular, in some species form Pseudomycelium ( Series of cells adhering after budding). Asexual reproduction – budding and fission and sexu reproduction by forming ascospore  The term Algae (L. alga- seaweed) is collectively used for Chlorophyll bearing non-vascular thalloid organisms.  Linnaeus (1754) first coined the term algae, which he plac Liverworts & lichen under class Cryptogamia of Conventio Kingdom.  But, in Whittaker’s classification, all members of algae are three kingdoms i.e. Monera (Blue Green Algae), Protista (D Dinoflagellates, Euglenoids) & Plantae (Green algae, Brow algae).  The study of algae is called Phycology or Algology. Characteristics of Algae: Algal cells are eukaryotic. Algae are photosynthetic organisms. Algae can be either unicellular or multicellular organisms. Algae lack a well-defined body, so, structures like roots, stems absent. Algae are found where there is adequate moisture. Reproduction in algae occurs in both asexual and sexual form Asexual reproduction occurs by spore formation. Algae are free-living, although some can form a symbiotic rela other organisms. Economic importance of Algae These eukaryotic aquatic organisms have no roots, fl and stem. It plays important role in alkaline reclaimin is used as a soil binding agent. They are economical important in a variety of ways which are discussed b 1. Food: Algae are a healthy source of carbohydrates proteins, and vitamins A, B, C, and E as well as the m like iron, potassium, magnesium, calcium, manganes zinc. Hence, people of countries like Ireland, Scotlan Sweden, Norway, North and South America, France, G Japan, and China uses it as a food ingredient. 2. Fodder: Algae are also used as fodder to feed livest cattle and chickens. 3. Pisciculture: In fish farming, Algae plays a very imp because it helps in the production process. Fish used zooplankton as food. It helps in maintaining the health marine ecosystem because algae are naturally absorb dioxide and also provide oxygen to the water. 4. Fertilizer: Algae are rich in minerals and vitamins. S used as liquid fertilizer which helps in the repairing lev present in the soil. 5. Reclaiming Alkaline: Blue-Green Algae helps in the r high concentration of alkalinity in the soil. 6. Binding Agent: Algae act as binding agents against na processes such as erosion. 7. Biological indicator: Algae are very sensitive. If there i change in the environment their pigments changes or m Water pollution is checked with the help of Algae like Eu Chlorella. These protists can be categorized into seven m algae, each with distinct sizes, functions, and c different divisions include: Euglenophyta (Euglenoids) Chrysophyta (Golden-brown algae and Diatom Pyrrophyta (Fire algae) Chlorophyta (Green algae) Rhodophyta (Red algae) Paeophyta (Brown algae) Xanthophyta (Yellow-green algae) Euglenophyta 45 genera, > 1,000 species, - Chlorophyll a, Chlorophyll b, Beta carotene, Xanthophylls. - Low to high pH waters, - Eutrophic to oligotrophic conditions. - Morphology: Spindle-shaped, no true cell walls, plasma membrane - Storage product: paramylon. - Asexual reproduction. - Nutrition: phototrophic, heterotrophic… 1.Euglenoids reproduce via longitudinal binary fission. 2.Binary fission is the process of asexual reproduction in which a single parent is divided into two new individuals. 3.The genetic material is duplicated before the division of the cytoplasm. Chlorophyta Chlorophyta is a taxonomic group (a phylum) c green algae that live in marine habitats. Some found in freshwater and on land (terrestrial hab Some species have even become adapted to th extreme environments, such as deserts, arctic hypersaline habitats, such as the Mediterranea  Green colour from chlorophyll a and b in the same pro as the 'higher' plants; beta-carotene (a yellow pigmen various characteristic xanthophylls (yellowish or brow pigments). Food reserves are starch, some fats or oils like highe Green algae may be unicellular (one cell), multicellula cells), colonial (living as a loose aggregation of cells) coenocytic (composed of one large cell without cross cell may be uninucleate or multinucleate). They have membrane-bound chloroplasts and nuclei. Biological Importance  The chlorophytes, because of their photosynthetic activity, m of the most important producers in the ecosystem. They are of starch and oxygen as a byproduct of photosynthesis.  They serve as food for many heterotrophs.  Many of them form symbiotic relationships with other group For example, they form lichens together with certain fungi.  Not all chlorophytes, though, are exclusively photosynthetic. are heterotrophic themselves. For example, the green alga P can become pathogenic, causing protothecosis (a disease) animals.  Chlorophytes have been used for commercial, industrial, and purposes. For instance, they served as a major source of bet which apart from using as a food coloring has been shown t preventing certain cancers, such as lung cancer. Reproduction  - Asexual reproduction may be by fission (splitting fragmentation or by zoospores (motile spores).  - Sexual reproduction is very common and may be (gametes both motile and same size); anisogamo and different sizes - female bigger) or oogamous motile and egg-like; male motile).  - Many green algae have an alternation of haploid phases. The haploid phases form gametangia (se reproductive organs) and the diploid phases form reduction division (meiosis). Some do not have an generations, meiosis occurring in the zygote. Plant Anatomy Prepared by Dr: Nivien Allam The aim of studied plant anatomy  Plant tissues and functions of each.  Anatomy of roots, stems and leaves ,also functions in plants.  Secondary thickening  Ecological groups and anatomy adaptations.  Tissues  TISSUES- a group of cells functioning together in some specialized activity. Tissues are classified according to the kind of the constituent cells into two types: Simple and Complex tissues. Simple tissue: is a tissue composed of only one type of cells Complex tissue: is composed of more than one type of cells which are associated together to perform a general function. Tissues  Tissues are also classified according to the stage of development of the constituent cells into two types: Permanent and Meristematic.  The meristematic tissues are young immature tissues composed of cells which are capable of division and continuous new cell formation. These tissues are mostly located in specific regions in the body of a higher plant called meristems. Tissues  The permanent tissue is the tissue composed of cells that have lost, at least temporarily, their capability of division. These cells are fully differentiated, mature and perform specific functions Meristematic Tissues  A meristematic cell is characterized by being active in division, new cell formation, having abundant cytoplasm, very small vacuoles, large nucleus, thin walls and no intercellular spaces. Meristematic tissues  Primary Apical Meristems  Secondary Vascular cambium Cork Cambium Primary meristematic tissues o located at the tip of root or stem and is called “ apical meristem”. There are primary meristems occur at the basis of internodes of some monocot plants and are referred to as “intercalary meristems”. oPrimary meristems are characterized by: 1- They develop as a result of division of special kind of meristems called the promeristem. 2- When they differentiate and mature they build up the primary body of the plant. Position of meristems  Apical meristems.  Lateral meristems.  Intercallary meristems  Apical meristem o The extreme tip is occupied by a group of young non-differentiated cells with similar diameters, thin walls, active cytoplasm, large nuclei and no intercellular spaces. This zone is called the promeristem, which constitutes the zone of cell division. Zone of cell enlargement  Protoderm: external layer, give epidermis.  Ground meristems: several layers, produce ground tissue, medullary rays and pith.  Procambium: circular zone of cells , primary vascular tissues. Secondary meristems 1- Originate from permanent tissue. 2- Give secondary tissues. e.g. cork cambium & intervascicular cambium. Objectives of today’s lecture:  Permanent tissues: are those which have lost, at least temporarily, their capability of cell division. They become differentiated to perform specific functions.  Cell differentiation involves modifications of cells. Flowering plants have 3 basic permanent tissue types  Dermal Cover surface of plant Protection  Ground  Vascular Conducting tissue Main Tissue Systems 1. Dermal 2. Vascular 3. Ground Dermal Tissue  Epidermis, Stomata, Hairs and Trichomes  Epidermis: Composed of a single protective layer of interlocked cells which over the entire surface of leaves, young roots and stems. It is covered by the cuticle which reduces water loss from epidermal cells.  Epidermal cells are often lobed and fitted together without any intercellular spaces forming a continuous layer. Epidermis Dermal Tissue:  Stomata: Gaseous exchange takes place between the intercellular spaces of subepidermal cells and the atmosphere. Types of stomata: Stomata dumb-bell shape Kidney shape Mechanism of stomatal movement: Sunken stomata with hairs without hairs Trichomes (hairs) Ground Tissue Cortex Endodermis Pericycle Medulla (pith) Medullary rays A- Parenchyma Characteristics: The cells of parenchyma are large, thin-walled, and usually have a large central vacuole. They are often partially separated from each other. They are usually stuffed with plastids. Types of Parenchyma Spongy parenchyma : Storage of food. Armed parenchyma :aeration Aerenchyma : oxygen storage Palisade : photosynthesis Chlorenchyma: photosynthesis Lignified parenchyma: Parenchyma  Least specialized plant cells  Thin and somewhat flexible cell walls  Living at maturity  Carry on most of the plant's metabolic functions  Generally have a large central vacuole  Most parenchyma cells have the ability to differentiate into other cell types under special conditions  Armed parenchyma Spongy parenchyma B- Collenchyma  Collenchyma cells have thick walls that are especially thick at their corners. These cells provide mechanical support for the plant. They are most often found in areas that are growing rapidly and need to be strengthened. The petiole ("stalk") of leaves is usually reinforced with collenchyma Collenchyma  Thicker primary cells walls (usually with uneven thickness)  Living at maturity  Role in support of herbaceous plants  Early development and adaptability to change in the rapidly growing organ especially those that increase in length. C- Sclerenchyma  The walls of these cells are very thick and built up in a uniform layer around the entire margin of the cell. Often, the protoplasts die after the cell wall is fully formed. Sclerenchyma cells are usually found associated with other cells types and give them mechanical support. Sclerenchyma  Thick secondary cell walls  Dead at functional maturity  Cannot increase in length - occur in parts of the plant which have quit growing in length  Two types - fibers and schlerids  Fibers - long, slender cells with a more or less regular secondary cell wall  Schlerids - shorter cells with an irregular shape Example - stone cells in pears and hard nut and seed shells Sclerenchyma  Sclerenchyma is a supporting tissue. Two groups of sclerenchyma cells exist: fibres and sclereids. Their walls consist of cellulose,hemicellulose and lignin. Sclerenchyma cells are the principal supporting cells in plant tissues that have ceased elongation. Sclerenchyma fibres are of great economical importance. Complex tissues  Xylem:  Phloem: Vessels Sieve cell Tracheids Sieve tube Parenchyma Companion cell Fibers Parenchyma Fibers Xylem Tissue  Primary xylem:  Secondary xylem: Vessels Vessels Tracheids Parenchyma Parenchyma Fibers Primary xylem Xylem Tissue  Thick secondary cell walls, often deposited unevenly in a coil-like pattern so that they may stretch  Dead at functionally maturity.  Involved in conduct of water and ions in the plant  Two types - tracheids and vessels  Tracheids - long, slender cells connected to each other by pits. Found in all vascular plants  Vessels - shorter, larger diameter cells with completely perforated cell wall ends. Found only in Angiosperms Primary xylem Secondary xylem: Xylem lignification Xylem Tissue  Vessels  Tracheids Fig. 38.13a Fig. 4.6 Fig. 38.13b Phloem Tissue A- Primary phloem: 1- Regular in monocots. 2- Irregular in dicots. Phloem Tissue Fig. 38.14a Phloem Tissue  Involved in transport of sucrose, other organic compounds, and some ions  Living at functional maturity Protoplast may lack organelles and nucleus, though  End walls connect to each other via sieve-plates  Phloem Tissue  Two types of cells in the phloem - sieve-tube members and companion cells Sieve-tube members - actual conduit for sucrose transport Companion cells - has a nucleus that may also control the sieve- tube element and may aid in sucrose loading Fig. 38.14b B- Secondary phloem Vascular Tissue Xylem Phloem Cambium Vascular Bundles  1- Collateral V B.  Open V B  Closed V B  2- Bicollateral V B  3- Radial V.B.  4- Concentric V.B. Vascular Bundles  In conjoint bundle xylem and phloem occur in the same bundle along the same radius.  In radial bundle, xylem and phloem occur in separate bundles, alternately. Radial bundles are characteristic features of the root.  In concentric bundle, xylem and phloem occur in the same bundle surrounding each other  Concentric V.B. oRadial V.B. Bicollateral V B Collateral V B. Secretory Tissue