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Port Said University Faculty of Science Botany Department Prof. Dr. Mohsen El Said Ibrahim Dr,Mona Mahmoud El Bous Professor of Microbiology Assistant professor of Plant taxonomy...

Port Said University Faculty of Science Botany Department Prof. Dr. Mohsen El Said Ibrahim Dr,Mona Mahmoud El Bous Professor of Microbiology Assistant professor of Plant taxonomy 1 Contents PLANT KINGDOM..................................................................................................................................... 3 Biodiversity............................................................................................. Error! Bookmark not defined. Why we study Systematics?...................................................................................................................... 6 Biological classification............................................................................................................................ 6 What is a classification system?.................................................................................................................... 8 Naming Organisms (Nomenclature)....................................................................................................... 11 Binomial Nomenclature.......................................................................................................................... 13 Linneaus’ Hierarchy (Classification Categories).................................................................................... 13 The three Domain System:...................................................................................................................... 23 Universal Phylogenetic Tree (The Tree of LIFE)................................................................................... 29 Viruses........................................................................................................................................................ 33 Chemical structure of virus..................................................................................................................... 36 virus shape: -........................................................................................................................................... 37 Viruses Classification............................................................................................................................. 39 Summary about General Properties of Viruses:...................................................................................... 40 Domain: Bacteria........................................................................................................................................ 45 Bacterial Structure................................................................................................................................ 46 Components of Bacterial cell.................................................................................................................. 47 Classification of bacteria:....................................................................................................................... 48 Bacteria can be classified according to the following............................................................................ 48 A) Classification of bacteria based on mode of nutrition................................................................... 49 B) Classification of bacteria based on optimum temperature of growth............................................. 50 D) Classification of bacteria based on optimum pH of growth........................................................... 51 E) Classification of bacteria based on salt requirement...................................................................... 51 F) Classification of bacteria on the basis of gaseous requirement...................................................... 52 G) Classification of bacteria based on morphology and arrangement................................................ 53 Classification of bacteria based on Gram staining:............................................................................. 54 Actinomycetes (Prokaryotic):.......................................................................................................... 57 Actinomycetes.................................................................................................................................... 57 Economic importance of bacteria....................................................................................................... 58 Role of Bacteria in Industry................................................................................................................ 58 General characters of Cyanobacteria.................................................................................................. 62 2  Advantages of Cyanobacteria............................................................................................................. 64.................................................................................................................................................................... 66 Kingdom: Fungi (Mycota).......................................................................................................................... 67 The main life cycle of a fungi:................................................................................................................ 70 Major characteristics of Fungi................................................................................................................ 72 Classification of fungi............................................................................................................................. 73 Kingdom: Protista....................................................................................................................................... 80 Algae....................................................................................................................................................... 81 General classification.......................................................................................................................... 81 What are the Algae.............................................................................................................................. 82 The general classification of groups within the algae......................................................................... 83 The difference between Algae and land plants:-................................................................................. 84 Reproductive diversity within the algae.............................................................................................. 88 Division: Chrysophytes (golden-brown algae) (Diatoms).................................................................. 90 Phaeophytes (brown algae)................................................................................................................. 90 Division :Dinophyta............................................................................................................................ 92 Division: Rhodophyta (Red Algae)..................................................................................................... 92 Human and ecological relevance:....................................................................................................... 94 Kingdom: Plantae........................................................................................................................................ 98 General characters................................................................................................................................... 98 Division: Pterophyta: Ferns.............................................................................................................. 108 Spermatophytes ‫(النباتات البذرية‬Phanerogamae(................................................................................ 112 practical part.......................................................................................................................................... 128 3  The Earth is populated by enormous numbers of different organisms. There is a great diversity among living organisms found on the planet earth.They differ in their structure, habit, habitat, mode of nutrition, and physiology. Biodiversity Definition To begin with, let’s find out what is biodiversity in the environment or what does biodiversity mean? Biodiversity definition (biology): Biodiversity can be defined as the broader term that circumvents all the types of biological forms that exist on this planet. The biodiversity science definition and biodiversity ecology definition are the same as above. This covers species diversity, genetic diversity, and ecosystem diversity. So, the three types of biodiversity are: Species diversity: Total number of different species (diverse species that form a part of a community. (Now we can explain what is species diversity) Genetic diversity: Total number of different genotypes (genetic variation) existing in the population of a community. Ecosystem diversity: Total number of variations that exist in a biodiverse ecosystem that’s defined by a given geographical location. (biodiversity in ecosystems) A 4  Why Is Biodiversity Important? We often are misled by the notion that it’s us humans who are the most important for the Earth to go around its normal course of life and death. Nature is self- sustainable and what makes it so is its rich biodiversity. Each member of biodiversity whether microscopic (soil biodiversity, bacterial or viral life form) or humongous (whale or elephant) has its own essence that is often undermined by us (humans) Some of the crudest examples of why biodiversity is important are: Biodiversity is the source of our food, shelter, and source of living. Biodiversity is what keeps us safe from different natural world disasters and pandemics. Biodiversity is what provides us with insights about art and literature. Biodiversity is the source of human being’s motivation to explore space About 1.8 million species have been given scientific names ; nearly 2/3 of these are insects but only about 1.7 million have actually been described including over 750,000 insects, about 250,000 flowering plants and 47,000 vertebrate animals. However, we may never know how many there really are because many of them will become extinct before being counted and described The tremendous diversity in life today is not new to our planet. The noted paleontologist Stephen Jay Gould estimated that 99% of all plant and animal species that have existed have already become extinct with most leaving no fossils. 5  The living organisms show a lot of similarities and common features so that they can be arranged into many groups. In order to understand them and study them systematically, these living organisms, mainly the plants and animals are grouped under different categories (Classification). Why we study Systematics? Systematics is the branch of Biology that deals with the diversity of organisms and their comparative and evolutionary relationships based on comparative anatomy, biochemistry, physiology and ecology; hence Systematic is the study and classification of living organisms. Generally; Classification is the grouping of information or objects based on similarities. Biological classification is the process by which living organisms are grouped into easily identifiable groups or categories based on some observable characters. 6 Why we classify the organisms? 1. To make things easier to find, identify, and study 2. To show relationship among various groups. 3. To show evolutionary trends and Biological evolution. Biological evolution: is the change of living things over time by selection or mutation..etc. OR is the process by which one species gives rise to another. 4. To help in interpreting the fossil records. 7 Systematic is made up of different sub-disciplines: taxonomy; classification, Nomenclature; Morphology and phylogeny. Definitions Taxonomy: - The branch of biology that names and groups organisms according to their characteristics and evolutionary history. Botany: A branch of biology studying plant life, including: structure, growth, taxonomy, systematics, reproduction, metabolism, physiology, biochemistry, development, diseases, ecology, and evolution of plants. What is a classification system? A classification system is a way to identify an organism and place it into the correct group of related organisms (based on similar characteristics). History of Classification Systems : The Greeks were the first people to show a scientific interest in the study of living things. 8 Ancient Greece Aristotle (384 BC to 322 BC) was the first to use a classification system. His classification system was based on structural differences that were seen. He classified all living things into two categories: plants and animals. Animals were classified on the basis of where they lived (Land, water, air). Plants were classified on the basis of their structure. (Herbs, shrubs, trees). Problems with this system: Frogs live in both water and on land Bats, birds and flying insects were grouped together Ray (1600’s-1700;s) – began to classify organisms by the internal anatomy of plants and animals. He also was the first to use the word “species”. 9  Species is the basic unit of classification and is defined as a group of organisms that is able to interbreed and produce fertile young. tiger lion Offspring is sterile mule donkey horse Concept of species With the ever increasing number of organisms, there was a need to name , classify and study an orderly system of classification. Carolus Linnaeus (1701-1778) was a Swedish biologist who : Established a simple system for classifying organisms Named organisms (scientific Nomenclature). All species are given a two-part name, a "binomial" Developed a Hierarchy (a ranking system) for classifying organisms that is the Basis for Modern Taxonomy. 10  He based his grouping on Structural similarities in organisms. Carolus Linnaeusʼ system allowed organisms to be grouped with similar organisms. ✓ He first divided all organisms into two Kingdoms. This was the same as Aristotle’s main categories.The two kingdoms consisted of: Plantae and Animalia. Naming Organisms (Nomenclature). Early Efforts at Naming Organisms Ancient people needed to communicate about which plants or animals were edible, poisonous or could be used medicinally, so they needed to identify and naming the 11 organisms. Common (vernacular) names varied from region to region and among different languages.. Problems with common naming include: 1. One organism having many common names. 2. Many different organisms having the same common name. 3. Many common names vary from region to region and country to country. What is the importance of using scientific names? Scientists world wide must rely on accurate information about organisms to avoid confusion. The first attempts at standard scientific names often described the physical characteristics of a species in great detail. Results in long names Difficult to standardize the names of organisms Different scientists described different characteristics. CarolusLinnaeus developed a two part naming system called Binomial Nomenclature.Using a single standard Latin name for each species avoids any chance of confusion. 12  Binomial Nomenclature is a system of scientific name i.e. each organism is given a two-part name. The first part of the name is the genus and the second part of the name is the species. The genus and species are always said and written together. The genus is capital and underline or italic and the species is lower-case and underline or italic. Genus and species named using Latin or Greek words. Why Latin? Because it was 1. The language of scholars at this time 2. A dead language i.e. does not continually change 3. Politically neutral and very descriptive Latin name of Human is Homo sapien or Homo sapien When a scientific name is written by hand, both parts of the name should be underlined, as Vicia faba or italic e.g Vicia faba. Linnaeus also created higher, more inclusive classification categories. Linneaus’ Hierarchy (Classification Categories) This Linnaean system of classification was widely accepted by the early 19th century and is still the basic framework for all taxonomy in the biological sciences today. Linnaeus’ classification system has seven levels. 13  Kingdom (broadest group) – Contains a group of related phyla Phylum - Contains a group of related classes Class - Contains a group of related orders Order - Contains a group of related families Family - Contains a group of related genuses Genus - Contains a group of related species Species (most specific) - Contains a group of related organisms are that are able to interbreed and produce fertile offspring. The Linnaean classification system has limitations. 1- It puts eukaryotes with prokaryotes together. 2- It also brings together non-photosynthetic Fungi with photosynthetic green plants. 3- The technology didn’t exist during Linneaus’ time. 4- Linnaean system based only on physical similarities 5- Linnaeus taxonomy doesn’t account for molecular evidence 14  6- The grouping of such diverse organisms into two Kingdoms is unsatisfactory and unrealistic Classification is always a work in progress. As biologists learned more about structure and function of different organisms, more kingdoms were added. ❖ Ernest Haeckel (1866) Proposed a THIRD kingdom ( Protista) The protista was a “dumping” ground to help deal with organisms that were neither animals nor plants. Ex: Euglena which had characteristics of both plants and animals, so placed within Kingdom Protista Euglena (plant -like Protista) Microscope Protists is defined as the Eukaryotes that are not animals, plants, or fungi. It may has single celled or multicellular, microscopic or very large and reproduce asexually and/or sexually. With the discovery of the MICROSCOPE in the 1600’s many new organisms were discovered. This was the basis for the change in the classification system. 15 The differences between prokaryotic cell and Eukaryotic cell prokaryotic cell Eukaryotic cell ❖ Recognition of different modes of nutrition 1. Autotrophs capture the light energy from sunlight and convert it to chemical energy they use for food. 16 2. Heterotrophs must get energy by eating autotrophs or other heterotrophs. 3. Decomposers, are heterotrophs that recycle dead organisms by breaking them down. More recent studies showed that Fungi (plant like) consists of hyphae ( mycelium), and obtain energy and nutrients by growing hyphae through the body of their food source.Hyphal tips secret and release enzymes which digest and breakdown the substrate into smaller, simpler, organic molecules, Product diffuses back into hypha and is used by the Fungus. Mode of nutrition of Fungi ( rhizopus) 17 Robert Whittaker (1969) {Five kingdom system} He Proposed a 5 Kingdom classification system based upon the following: a. Number of cells b. Presence or absence of a nucleus c. Mode of Nutrition. This classification system organizes the diversity of life into the kingdom Monera, which comprises all prokaryotes, and four kingdoms of eukaryotes: Protista, Plantae, Fungi, and Animalia 18  1- Kingdom : Monera Bacteria Cyanobacteria (Blue green algae) Monera are the only kingdom composed of prokaryotic organisms, they have a cell wall, and lack both membrane-bound organelles and multicellular forms. e.g. Bacteria, blue-green bacteria (cyanobacteria-cyanoprokaryta) 2- Kingdom: Fungi: Rhizopus Mushroom Organisms from this kingdom were originally classified as plants, but fungi are not photosynthetic and are heterotrophic, so they became a separate kingdom. 19 Fungi are eukaryotic, heterotrophic, usually multicellular group having multinucleated cells enclosed in cells with cell walls. They obtain their energy by decomposing dead and dying cells of organisms and absorbing their nutrients from those organisms. Fungi are made up of a network of tubes called Hyphae (mycelium) Examples: Mushrooms, moulds, yeast. 3- Kingdom: Protista The most ancient eukaryotic kingdom, protists include a variety of eukaryotic forms. Perhaps they are best defined as eukaryotes that are NOT fungi, animals, or plants. Protists are generally divided into three groups based on how they get their food: ❖ Animal-like (consume other organisms) heterotrophs: single-celled. It is not animals because animals are multicellular and animal like Protista are single- celled ❖ Plant-like (make own food) (autotrophs), single-celled, colonial (live 20  together in colonies), or multicellular. Not plants because they have no roots, stems, or leaves (have no vascular tissues i.e. xylem and phloem) ❖ Fungus-like (decompose other organisms): Heterotrophs and can move at some point in their life cycle whereas fungi cannot Examples: Paramecium, amoeba, some algae, and slime moulds. 4- Kingdom:Plantae Plants are immobile, multicellular eukaryotes that produce their food by photosynthesis and have cells encased in cellulose cell walls. Examples: Ferns, pine trees and roses 5- Kingdom: Animailia Animals are multicellular, heterotrophic eukaryotes that are capable of mobility at some stage during their lives, and that have cells lacking cell walls. Examples: Humans, worms, spiders. 21  The characteristics of 5 kingdoms that are listed below. Kingdom Characteristic Nutrition Example Small, simple single-cell, Absorb food (some Bacteria & 1-Monera (sometimes chains photosynthetic) cyanobacteria Large, complex single cell All types Protozoans, 2-Protista (sometimes chains or algae colonies) Multicellular filamentous Absorb food Molds and 3-Fungi form with specialized mushrooms complex cells Multicellular form with Photosynthesize Mosses, ferns 4- Plantae specialized complex cells food flowering plants Multicellular form with Ingest food Sponges, 5- Animalia specialized complex cells worms, insects, fish. Due to recent discoveries, the higher ranks of classification have changed. ❖ Carl Woese,1977 Six Kingdom System and Three Domain of the Life In the 1970’s, microbiologist Carl Woese, among other researchers conducted studies and concluded that a group of prokaryotic microorganisms called Archaebacteria are separate from other Monerans.(based on ribosomal RNA) Therefore, they decided to split kingdom Monera into two separate kingdoms: Ribosomal RNA is used to study distantly related species because: 1. Many conservative regions 2. Lower mutation rate than most DNA Under this system, organisms are classified into three domains and six kingdoms. 22 He reported that the Archaebacteria comprised "a kingdom" of life as distinct from bacteria. Having defined Archaea as a new "kingdom" (later domain) which were neither bacteria nor eukaryotes. His three-domain system, based on phylogenetic relationships rather than obvious morphological similarities. The current system, the Three Domain System, groups organisms primarily based on differences in ribosomal RNA structure. Ribosomal RNA is a molecular building block for ribosomes. A phylogenetic tree based on rRNA data showing Woese's three-domain system The three Domain System: ❖ Archaea: prokaryotes; extremophiles ❖ Eubacteria: prokaryotes; true bacteria ❖ Eukarya: eukaryotes Protista, Fungi, Plantae and Animalia 23 The domains are Archaea, Bacteria, and Eukarya. The kingdoms are Archaebacteria (ancient bacteria), Eubacteria (true bacteria), Protista, Fungi, Plantae, and Animalia – The Archaea and Bacteria domains contain prokaryotic organisms. These are organisms that do not have a membrane bound nucleus. – Archaea appear to be more related to eukaryotes—organisms with complex cells containing nuclei-than to bacteria. Archaea do not have nuclei, but their cell structure is different from that of bacteria. Comparing ribosomal RNA base sequences, Woese and his colleagues also showed that organisms belonging to Eukarya are more similar to Archaea than they are to Bacteria.. Archaebacteria Cell walls chemically different from bacteria Differences discovered by studying RNA Known for living in extreme environments ( high or low pH ,High or low temperature) 24  Differences between Eubacteria and Archaebacteria Eubacteria are classified under the Bacteria domain and archaebacteria are classified as Archaeans. The Eukaryota (Eukarya) domain includes eukaryotes, or organisms that have a membrane bound nucleus. This domain is further subdivided into the kingdoms Protista, Fungi, Plantae, and Animalia. ◼ NOTE: Domains are the largest group of classification. Kingdoms are just below domains. ◼ A series of 8 levels of classification are used. 25 All six kingdoms are separated into the THREE DOMAINS of Life. A. Domain Bacteria – Kingdom Eubacteria B. Domain Archaea – Kingdom Archaebacteria C. Domain Eukarya – Kingdoms Animalia, Plantae, Protista and Fungi. 26 The following table summarizes the characteristics of the three Domains: DOMAIN CHARACTERISITCS lack a nuclear envelope Bacteria circular chromosome exclusively single-celled (e.g., bacteria) lacks membrane-enclosed organelles growth inhibited in presence of antibiotics lack a nuclear envelope circular chromosome exclusively single celled Archaea lacks membrane-enclosed organelles growth not inhibited in presence of antibiotics some species thrive at temperatures in excess of 100 oC have a nuclear envelope lacks circular chromosome Eukaryota includes both single celled and multicellular has membrane-enclosed organelles growth not inhibited by antibiotics The modern, six-kingdom system has evolved from the earlier systems. Keep in mind that as we learn more about life on Earth, this system will most likely be revised. 27 Cavalier-Smith 1987 ( Two Domains and eight Kingdoms system.) Eight Kingdom System (Cavalier-Smith’s Concept) The Kingdom Protista was still too diverse to be taxonomically useful. Cavalier- Smith, using ultra-structural characteristics as well as rRNA sequences, divides all organisms into two Domaina and eight kingdoms. By 1993, he reduced the total number of eukaryote kingdoms to six. He also classified the domains Eubacteria and Archaebacteria as kingdoms, adding up to a total of eight kingdoms of life. 1. Eubacteria, 2. Archaebacteria 3. Fungi 4. Plantae 5. Protozoa 6. Chromista 7. Archezoa. 8. Animalia 1. Domain : Bacteria: include Eubacteria & Archaea. Domain : Eukaryota: Four eukaryotic Kingdoms and Two new kingdoms namely Archezoa &Chromista which previously treated as protista and Cavalier-Smith's new classification scheme retained the plant, animal and fungal kingdoms from the traditional five kingdom model. It also split the kingdom Monera into the two groups, eubacteria and archaebacteria, as proposed by Woese. In 28  addition it split the kingdom protists into three new kingdoms: archezoa, protozoa, and chromista. Cavalier-Smith et al.2015 (2 Domains (Empires) & 7 Kingdom) They are proposing a two-superkingdom (Prokaryota and Eukaryota), seven- kingdom Universal Phylogenetic Tree (The Tree of LIFE) Modern classification is based on evolutionary relationships A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities-their phylogeny-based upon similarities and differences in their physical or genetic characteristics. The taxa joined together in the tree are implied to have descended from a common ancestor. 29 A speculatively rooted tree for rRNA genes, showing the three life domains 30 Classification systems change as scientists learn more. 31 Viruses 32  Viruses Viruses are still biologists’ puzzle because they show both living and nonliving characters. Hence viruses are regarded as a separate entity. It is not taken into account in Whittaker’s five kingdom classification. Viruses are now defined as ultramicroscopic, disease causing intra cellular obligate parasites. Brief history of discovery Viruses were not known to biologists for a long time due to their ultramicroscopic structure, they are the smallest things, though their presence was apparent by infectious diseases which were proved not due to bacteria. It attracted the attention of investigators only in the 19th century when a virus called tobacco mosaic virus (TMV) caused severe damage to commercially important tobacco crop. Mayer demonstrated that the disease could be transmitted just by applying the sap of infected leaf to the leaf of healthy plant. He thought that the disease was due to a bacterium. It was then the Russian biologist Iwanowsky (1892) who demonstrated that the sap of infected leaves even after passing through bacterial filter remained infective, ruling out the bacterium as the causative agent. Dutch microbiologist Beijerinck (1898) confirmed the findings of Iwanowsky and called the fluid “contagium vivum fluidum” which means contagious living fluid. This was later on called virion (poison) and the disease causing agent as virus. W.M. Stanley (1935), the American biochemist, isolated virus in crystalline form and demonstrated that even in that state it maintained the infectivity. This marked the beginning of a new branch of science called virology. IMPORTANT NOTES Viruses are not classified in a kingdom. Viruses are the smallest things. Much smaller than most prokaryotes. We also cannot say that viruses are the smallest living things or organisms, as viruses 33  do not meet the definition of living or of an organism. Viruses are considered at the borderline of living and non-living because they show both the characteristics of a living and a non-living. As they react like non-living in the free atmosphere but when they enter in the body of a living organism then they show the features of a living organism (Mrs C Gren) and start reproduction. 34 General characteristics Viruses are ultramicroscopic particle (molecule) and can cause diseases in plants and animals (Ex: colds, rabies, AIDS, flu). They are very simple in their structure. They are composed of nucleic acid surrounded by a protein coat. Nucleic acid can be either RNA or DNA, but never both. They have no cellular organization and have no machinery for any metabolic activity. They are obligate intracellular parasites and they multiply within their host cells. Once outside the host cell they are completely inactive. Viruses are widely distributed in nature, causing infection of man, animal, insects, and bacteria, many hundreds of viruses have been described. Physical properties of viruses (Virus Size and shape) Viruses are very minute particles that they can be seen only with a powerful electron microscope. They are much smaller than bacteria. Indeed the largest virus is half the size of the smallest bacterium. They are measured in millimicrons (1 millimicron = 35 1/1000micron). (1micron – 1/1000 millimeter). Generally, they vary from 2.0 mm to 300 mm in size. Viruses are submicroscopic particles that can be seen only electron microscope. Viruses range in size from about 20 to 750 nm (nanometers) in diameter (1 nanometre = 10-9 meters), which is 45,000 times smaller than the width of a human hair. Electron Microscope Shape of virus under Scanning electronic microscope Chemical structure of virus Viruses are composed of one type of nucleic acid (either RNA or DNA), surrounded by a outer shell coat capsid, made of protein called a-capsid. The capsid protects the genome and gives the virus its shape. Some viruses have additional structural features, such as the envelope of animal viruses or the tail of bacteriophages. The capsid is the outer protein coat. It is protective in function. It is often composed of many identical subunits called capsomeres. Some of the viruses have an outer covering called envelope eg. HIV. They are called enveloped viruses. Others are called naked viruses or non- enveloped viruses. The nucleic acid forms the central core. Unlike any living cell a virus contains either DNA or RNA, but never both. The infective nature of the virus is attributed to the nucleic acid while host specificity is attributed to the protein coat. 36  Virus structure When a single virus is in its complete form and has reached full infectivity outside of the cell and biologically inert, it is known as a virion. virus shape: - A virus structure can be one of the following: icosahedral, enveloped, complex or helical. 1. Helical virus Helical viruses consist of nucleic acid surrounded by a hollow protein cylinder or capsid is made by proteins arranged in a circular fashion. An example of a virus with a helical symmetry is the tobacco mosaic virus. 2. Round shape: - e.g. Herpes virus 3. Rod shape: - e.g. Tobacco mosaic virus 4. Icosahedral (Polyhedral ) virus These viruses appear spherical in shape, but a closer look actually reveals they are 37 icosahedral and consist of nucleic acid surrounded by a polyhedral (many-sided) shell or capsid. The genetic material is fully enclosed inside of the capsid. Examples of viruses with an icosahedral structure are the poliovirus, rhinovirus, and adenovirus. 5. Complex (Binal) virus ( Bacteriophage) These virus structures have a combination of icosahedral and helical shape and may have a complex outer wall or head-tail morphology. The head of the virus has an icosahedral shape with a helical shaped tail. The bacteriophage uses its tail to attach to the bacterium,. The Pox virus is one of the largest viruses in size and has a complex structure with a unique outer wall and capsid. 38  Bacteriophage Bacteriophage infect E. coli bacteria 6. Envelope virus: It consists of nucleic acid surrounded by either a helical or polyhedral core and surrounded by a lipid bilayer membrane, meaning the virus is encased or enveloped. The most well-known examples of enveloped viruses are the influenza virus, Hepatitis C and HIV. Viruses Classification Virus can be grouped together by 1. Their shape 2. Type of disease they cause 3. Life cycle 4. Type of genetic material they contain Viruses and living cell Viruses must infect a living cell in order to grow and reproduce. they also take advantages of host respiration, nutrition and all the other functions that occur in living things, therefore, viruses are considered to be parasites. 39 How do viruses reproduce ? 1. Virus injects itself into a living cell 2. Protein coat is discarded 3. Hereditary material takes over the cell’s activities 4. Virus reproduces and the cell fills 5. Cell splits open 6. Viruses leave the cell and attack new cells. Summary about General Properties of Viruses: Obligate intracellular parasites of all organisms ( bacteria, protozoa, fungi, 40  algae , plants and animals.) Are not cells but resemble complex molecules composed of protein and nucleic acid Do not exhibit the characteristics of life, but can regulate the functions of host cells. Inactive macromolecules outside (crystals) the host cell and active only inside host cell. Molecules on virus surface impart high specificity for attachment to host cell (they have a specific host range, sometimes specific to one species or even limited cell types of one species) Multiply by taking control of host cells genetic material and regulating the synthesis and assembly of new viruses. They are metabolically inert, and consequently are not susceptible to antibiotic or other agents that act against the metabolic pathways of microorganisms. Infect all groups of living things and produce a variety of diseases. Therefore; Viruses are Obligate, Intracellular, Parasite Example: - Corona virus The SARS-CoV-2 virus consists of four different proteins and a strand of RNA. The most prominent feature, a trimer formed by the “Spike” protein, sticks out from the membrane and gives the virus its distinctive “corona” structure. Two other proteins, envelope protein and membrane protein, reside in the membrane between these spikes, providing structural integrity. Inside the membrane, a fourth protein, nucleocapsid, acts as a scaffold surrounding the 29,900 nucleotides of RNA making 41 up the viral genome. Corona virus: one of the largest among RNA viruses. Member viruses of the family Coronaviridae are enveloped, 80–220 nm in size, often spherical (coronaviruses). Corona virus (COVID 19) Significance of Viruses 1. Viruses are a kind of biological puzzle to biologists since they are at the threshold of living and non-living things showing the characteristics of both. 2. Viruses are very much used as biological research tools due to their simplicity of structure and rapid multiplication. They are widely used in research especially in the field of molecular biology, genetic engineering, medicine etc. 3. Viruses are used in eradicating harmful pests like insects. Thus they are used in Biological Control Programmes. 4. Plant viruses cause great concern to agriculturists by their pathogenic nature. Bacteriophages attack the N2 fixing bacteria of soil and are responsible for reducing the fertility of soil. 5. In industry, viruses are used in preparation of sera and vaccines. 42 Bacteria 43 Domain: Archaea Kingdom: Archaebacteria The Archaea (originally called archaebacteria and containing prokaryotes that live mostly in extreme environments.) This scheme is currently accepted by most biologists. Archaea can live in extreme environmental conditions like absence of oxygen (anaerobic), high salt condition, high temperature like 800c or above and highly acidic soils. (very hot, acidic/basic, sulfurous, etc Discovery of Archaea Relatively recently (1970s), largely as a result of the work of Carl Woese and his group on 16S ribosomal RNA analysis (Section 10.4.4), a startling discovery was made. A number of the microorganisms that had long been called bacteria were actually examples of an entirely different form of life. This new group was at first called Archaebacteria, and the true bacteria were then called Eubacteria. However, in view of how different the two groups truly are (more different than plants are from animals, for example), microbiologists now refer to the two as Archaea and Bacteria. There was considerable opposition at first to the idea that these were such distinct groups. Even today, when it is widely accepted, many people still refer to members of Archaea as ‘‘bacteria.’’ However, since both are prokaryotes, this term can, when needed, be used to refer to the two together. ✓ RNA and cell wall are much different from other, true bacteria Subdivided into 3 groups: includes three kingdoms. Archaea includes the methanogenic bacteria that produce methane gas in a wastewater treatment plant’s anaerobic digester. Many of the archaea are notable for the harsh chemical and physical environments in which they thrive. Because of this it is thought that Archaea may be relics of the earliest forms of life that still exist today. Groups 44 included in Archaea are methane producers, hyperthermophiles, extreme halophiles, and sulfur reducers. o Methanogens ✓ Live in anaerobic environments (no oxygen) ✓ Get energy by changing H2 & CO2 into methane gas ✓ Found in swamps, sewage treatment plants, digestive tracts of animals ✓ Break down cellulose in a cow’s stomach ✓ digest cellulose into forms nutritious to the animal ✓ Produce methane gas o Extreme Halophiles ✓ Live in very salty water ✓ Use salt to generate ATP (energy) ✓ Dead Sea, Great Salt Lake inhabitants o Thermoacidophiles ✓ Live in extremely hot environments ✓ Found in volcanic vents, hot springs, cracks on ocean floor that leak acid Domain: Bacteria Kingdom: Eubacteria Bacteria are microscopic, single-celled microbes and prokaryotic organisms that thrive in diverse environments. Bacteria are single celled. The cell structure is simpler than that of other organisms as there is no nucleus or membrane bound organelles. In general, bacteria are between 0.2 and 2.0 µm (10 -6 m) (1 micrometer (µm) is one-thousandth of a millimeter). Bacteria are ubiquitous. They are found in all environments, where organic matter is present, they can live in soil, the ocean and inside the human gut and also they are found in air, water, soil and also in or on 45 the bodies of plants and animals. Some of the bacteria live as commensals (eg. Escherichia coli in the human intestine) and some live as symbionts (eg. Rhizobium) in the root nodules of leguminous plants. Several of them cause diseases in plants, animals and human beings. Bacterial Structure Bacteria (singular: bacterium) are classified as prokaryotes, which are single-celled organisms with a simple internal structure that lacks a nucleus, and contains DNA that either floats freely in a twisted, thread-like mass called the nucleoid (meaning nucleus-like) , or in separate, circular pieces called plasmids. Ribosomes are the spherical units in the bacterial cell where proteins are assembled from individual amino acids using the information encoded in ribosomal RNA. Bacterial cells are about one-tenth the size of eukaryotic cell 0.5–5.0 micrometres in length and approximately 0.5 to 1 micron in diameter. 46 Components of Bacterial cell 1. Capsule - Some species of bacteria have a third protective covering, a capsule made up of polysaccharides. It keeps the bacterium from drying out The capsule is a major virulence factor in the major disease-causing bacteria, 2. Cell Wall - Each bacterium is enclosed by a rigid cell wall composed of peptidoglycan, a protein-sugar (polysaccharide) molecule. The wall gives the cell its shape and surrounds the cytoplasmic membrane, protecting it from the environment. It also helps to anchor appendages like the pili and flagella, which originate in the cytoplasm membrane and protrude through the wall to the outside. 3. Cytoplasm - The cytoplasm, or protoplasm, of bacterial cells is where the functions for cell growth, metabolism, and replication are carried out. It is a gel-like matrix composed of water, enzymes, nutrients, wastes, and gases and contains cell structures such as ribosomes, a chromosome, and plasmids. bacteria do not have a membrane enclosed nucleus. The chromosome, a single, continuous strand of DNA, is localized, but not contained, in a region of the cell called the nucleoid. All the other cellular components are scattered throughout the cytoplasm. 4. plasmids, are small, extrachromosomal genetic structures carried by many strains of bacteria. Like the chromosome, plasmids are made of a circular piece of DNA. 5. Cytoplasmic Membrane - A layer of phospholipids and proteins, called the cytoplasmic membrane, encloses the interior of the bacterium, regulating the flow of materials in and out of the cell. 6. Flagella - Flagella (singular, flagellum) are hair like structures that provide a means of locomotion for those bacteria that have them. 47  7. Nucleoid - The nucleoid is a region of cytoplasm where the chromosomal DNA is located. It is not a membrane bound nucleus. The chromosome, a single, continuous strand of DNA 8. Pili - Many species of bacteria have pili (singular, pilus), small hairlike projections emerging from the outside cell surface. These outgrowths assist the bacteria in attaching to other cells and surfaces, such as teeth, intestines, and rocks. 9. Ribosomes - Ribosomes are microscopic spherical units "factories" found in all cells, including bacteria. They translate the genetic code from the molecular language of nucleic acid to that of amino acids. Reproduction of Bacteria Asexually by binary fission Classification of bacteria: Bacteria can be classified according to the following A. Based on mode of nutrition B. Based on optimum temperature requirement for growth C. Based on optimal pH for growth D. Based on salt concentration E. Based on gaseous requirement F. Based on morphology G. Based on flagella H. Based on gram staining I. Based on spore 48 A) Classification of bacteria based on mode of nutrition 1. Phototrops: including the green bacteria and purple bacteria, whose energy for growth is derived from sunlight 2. Chemotrops: Those bacteria gain energy from chemical compounds. They cannot carry out photosynthesis 3. Autotrops: Those bacteria which uses carbon dioxide as sole source of carbon to prepare its own food. 49 4. Heterotrops: Those bacteria which uses organic compound as carbon source. They lack the ability to fix CO2. Most of the human pathogenic bacteria are heterotropic in nature. Some heterotrops are simple, because they have simple nutritional requirement. Heterotrophs must get their food from a source of pre-formed organic matter: § (A) Saprobes- feed on the remains of dead plants and animals. § (B) Parasites - live on or in the organism and cause disease. For example, Salmonella typhi § (C) Symbiotic bacteria Rhizobacteria grow in root nodules of legumes (soybeans, peanuts) and they Fix N2 from air into usable ammonia B) Classification of bacteria based on optimum temperature of growth 1. Psychrophiles: Bacteria that can grow at 0°C or below but the optimum temperature of growth is 15 °C or below and maximum temperature is 20°C are called psychrophiles. 2. Mesophiles: Those bacteria that can grow best between (25-40) 0C but optimum temperature for growth is 37 0C. Most of the human pathogens are mesophilic in nature 4. Thermophiles: Those bacteria that can best grow above 45 0C and in hot springs. 5. Hyperthermophiles: Those bacteria that have optimum temperature of growth above 80 0C. Mostly Archeobacteria are hyperthermophiles. 50 D) Classification of bacteria based on optimum pH of growth 1. Acidophiles: Those bacteria that grow best at acidic pH The cytoplasm of these bacteria are acidic in nature. 2. Alkaliphiles: Those bacteria that grow best at alkaline pH with optimum pH of growth is 8.2 3. Neutriphiles: Those bacteria that grow best at neutral pH (6.5-7.5). Most of the bacteria grow at neutral pH. Note. Most of the bacteria grow at neutral pH. E) Classification of bacteria based on salt requirement 51 1. Halophiles: Those bacteria that require high concentration of NaCl for growth. 2. Halotolerant: Bacteria (most bacteria) do not require NaCl but can tolerate low concentration of NaCl in growth media F) Classification of bacteria on the basis of gaseous requirement 1. Obligate aerobes: Those bacteria that require oxygen and cannot grow in the absence of O2. 2. Facultative anaerobes: Those bacteria that do not require O2 but can use it if available. Growth of these bacteria become better in presence of O2 3. Aerotolerant anaerobes; Those bacteria do not require O2 for growth but can tolerate the presence of O2. Growth of these bacteria is not affected by the presence of O2. 4. Microaerophiles: Those bacteria that do not require O2 for growth but can tolerate low concentration of O2. 5. Obligate anaerobes: Those bacteria that can grow only in absence of Oxygen, they unable to use O2 as electron acceptor. Oxygen is harmful to obligate anaerobes 52  These bacteria have only fermentative type of metabolism G) Classification of bacteria based on morphology and arrangement The rigid bacterial cell wall determines shape of a cell. Typical bacterial cells are spherical (Cocci), straight rods (Bacilli) or rods that are helically curved (spirilla), some bacterial cells are pleomorphic i.e. they can exhibit a variety of shapes eg. Arthrobacter Cocci bacteria appear in several characteristic arrangements depending on their plane of division. 1. Coccus: These bacteria are spherical or oval in shape On the basis of arrangement, cocci are further classified as: i) Diplococci: Cells divide in one plane and remain attached in pairs ii) Streptococci: Cells divide in one plane and remain attached to form chains. iii) Staphylococci: Cells divide in three planes, in an irregular pattern, producing bunches of cocci. iv) Tetracocci: Cells divide in two planes and form group of four cells. v) Sarcina: cells divide in three planes, in a regular pattern, producing a cuboidal arrangement of cells. 2. Bacilli (Rod-shape): These are rod shaped bacteria On the basis of arrangement, bacilli are further classified as: i) Coccobacilli. ii) Streptobacilli: chain of rod shape bacteria. 53  iii) Comma shaped. 3- Spirochaetes: They are spiral shaped bacteria Different morphology of bacteria. Classification of bacteria based on Gram staining: One of the most important and widely used differential staining technique in microbiology is called Gram staining. This technique was introduced by Christian Gram (1884). In this process the fixed bacterial smear is subjected to the following staining reagents in the order, crystal violet, iodine solution, alcohol (decolorizing agent) and safranin. Bacteria stained by the gram method fall into two groups: 54 1. Gram positive bacteria: Gram positive bacteria which retain the crystal violet and hence appear deep violet in color, cell wall of these bacteria is composed of peptidoglycan layer only. 2. Gram negative bacteria: Gram negative bacteria which loses the crystal violet and counterstained by safranin and hence appear pink in colour, cell wall of these bacteria is composed of Peptidoglycan and outer membrane. The classification of bacteria into Gram positive and negative is mainly based on difference in cell wall structure: 1- The cell wall of Gram negative bacteria contains a higher percentage of lipids than do Gram positive bacteria. 2- The cell walls of gram positive bacteria, has different composition from Gram negative bacterial cell wall as it has lower lipid content, They are composed predominantly of peptidoglycan. This combines together to create an incredibly strong cell wall. The additional component in a gram positive cell wall is teichoic acid, a glycopolymer, which is embedded within the peptidoglycan layers. The 55 cell wall of Gram positive bacteria and peptidoglycan layer 56  Actinomycetes (Prokaryotic): They have filamentous or branching structure They resemble more closely to Fungi than bacteria Actinomycetes are gram positive bacteria which comprise a group of branching unicellular microorganisms. They form a threadlike net called a mycelium that bears chains of spores at maturity. The mycelium is of two kinds viz., substrate mycelium and aerial mycelium. Among actinomycetes, the streptomycetes are the dominant. The non‐streptomycetes are called rare actinomycetes, comprising approximately 100 genera. Streptomycetes are best known for their ability to produce antibiotics. Substrate mycelium Actinomycetes 57 Economic importance of bacteria 1. Sewage disposal: Organic matter of the sewage is decomposed by saprotrophic bacteria. 2. Decomposition of plant and animal remains: Saprotrophic bacteria cause decay and decomposition of dead bodies of plants and animals. They release gases and salts to atmosphere and soil. Hence these bacteria are known as nature’s scavengers. 3. Soil fertility: 1) Nitrogen fixing bacteria such as Azotobacter and Clostridium and Rhizobium (a symbiotic bacterium) are capable of converting atmospheric nitrogen into organic nitrogen. All these activities of bacteria increase soil fertility. 4- Recycling of matter Bacteria play a major role in cycling of elements like carbon, oxygen, Nitrogen and sulphur. Thus they help in maintaining environmental balance. As biological scavengers they oxidize the organic compounds and set free the locked up carbon as CO2. The nitrogenous organic compounds are decomposed to form ammoniawhich is oxidized to nitrite and nitrate ions by the action of nitrifying bacteria.These ions are used by higher plants to synthesize nitrogenous organic compounds.The nitrogenous compounds are also oxidized to nitrogen by denitrifying bacteria. Role of Bacteria in Industry 1) Dairy Industry: Lactic acid bacteria e.g.(Streptococcus lactis) are employed to convert milk sugar lactose into lactic acid. 58  2) Methanogenesis bacteria make methane (natural gas) as a waste product. They are found in swamp sediments, sewage, and in buried landfills. In the future, they could be used to produce methane as a byproduct of sewage treatment or landfill 3) Vinegar: Vinegar (Acetic acid) is obtained by the activity of acetic acid bacteria(Acetobactor aceti). This bacterium oxidizes ethyl alcohol obtained from molasses by fermentation to acetic acid or vinegar. 4) Alcohols and Acetone:- Butyl alcohol, methyl alcohol and acetone are prepared from molasses by the fermentation activity of the anaerobic bacterium Clostridium acetobutylicum. 5) Retting of fibres:- The fibres from the fibre yielding plants are separated by the action of bacteria like Clostridium species. This is called retting of fibres. Role of bacteria in medicine 1) Antibiotics: Antibiotics such as bacitracin (Bacillus subtilis) and Actinomycetes are obtained from bacterial sources. 2) Vitamins: Escherichia coli ( E.coli) living in the intestine of human beings produce large quantities of vitamin K and vitamin B complex. Vitamin B2 is prepared by the fermentation of sugar by the action of clostridium species. Role of bacteria in genetic engineering 1) (PCR) Polymerase chain reaction: Thermophiles contain genes for heat-stable enzymes that may be of great value in industry and medicine. An example is taq polymerase which is used to make large numbers of copies of DNA sequences in a DNA sample. It is invaluable to medicine, biotechnology, and biological research. Annual sales of taq polymerase are roughly half a billion dollars. 2) The transfer of human insulin genes into bacteria and commercial production 59  of insulin has already commenced by plasmid Role of bacteria in biological control Certain Bacillus species such as B. thuringiensis infect and kill the caterpillars of some butterflies and related insects. Since the bacteria do not affect other animals or plants they provide an ideal means of controlling many serious crop pests. Harmful effects of bacteria Bacteria are causing serious diseases in plant, animals and human. 60 61 Domain: Bacteria Kingdom: Eubacteria Phylum: Cyanobacteria ( Blue green algae) General characters of Cyanobacteria 1. Cyanobacteria ‘formerly known as’ Blue Green Algae. (Cyano = blue that they are more closely related to prokaryotic bacteria than eukaryotic algae. 2. Cyanobacteria have the ability to tolerate a wide range of conditions Marine –Fresh Water, Hot Springs, Terrestrial – soil flora 3. They have different pigments (chlorophyl a, phycobiliproteins – phycoerythrin and phycocyanin (Blue green Color) 4. Storage food as glycogen 5. Cell Walls – amino acids, sugars 6. Gram negative (–ve ) stain 62 7. They range in diameter from about 1 – 10 µm. 8. Found in marine sediments and freshwater lakes, soils. 9. Live in stressed environments – chemically and temperature (aerobic and anaerobic with light present). 10.The external structure can range from unicellular or colonial to branched or unbranched and filamentous the cyanophytes possess no flagellated or ciliated cells. It moves by gliding. 11.Unicell – with mucilaginous envelope, Colonies, Filaments – uniserate in a single row. 12.Mucilaginous sheath layer of mucilage outside of the cell wall. Function – protects cells from drying and involved in gliding. 13.Can live in fluctuating environments of aerobic and anaerobic with light present. 14.Nostoc consists of vegetative cell and Heterocyst (thick walled cell). Larger than vegetative cells. Heterocyst provides the anerobic environment for N fixation. Anabaena Spirulina Nostoc Reproduction Asexual § Fragmentation- filament breaks into 2 parts, each of which forms a new thallus. § Hormogonia- short sections of a trichome detach and form a new thallus. § Akinetes- resting spores; cells that are resistant to unfavorable conditions. 63  § Binary Fission- division of a single-celled individual into two new single- celled individuals. Advantages of Cyanobacteria 1. Nitrogen fixation: convert unavailable atmospheric nitrogen to available form. (IMPORTANT because atmospheric N2 is unavailable to most living organisms because breaking the triple bond is difficult) 2. Commercial food source (Spirulina). For Human provided in tablets, capsules, and liquid Considered to enhance the nutritive value of pastas, snack foods, candy bars or gums, and beverages. 3. Nitrogen Fixation: ONLY cyanobacteria and prokaryotic bacteria can fix nitrogen. Of these two organisms only cyanobacteria evolve oxygen during photosynthesis. Nitrogen is a limiting nutrient necessary for the production of amino acids = building blocks of life. Important because nitrogenase (enzyme involved in fixing nitrogen) is inactivated by O2. 4. Lichens- Blue green algae live in a Symbiotic relationship with fungi. Together, the algae and the fungus form a living unit. The algae through photosynthesis produce sugar as a food source, and the fungus provides support and protection from drying. Lichens 64 Disadvantages of Cyanobacteria 1-Cyanotoxins in Cyanobacteria a. Neurotoxins – block neuron transmission in muscles (Anabaena, Oscillatoria) b. Hepatotoxins – inhibit protein phosphatase, cause liver bleeding. Found in drinking water. (Anabaena, Oscillatoria, Nostoc) 2- Cause water bloom: they release may discolour the water, deplete its oxygen content, poison aquatic animals and waterfowl, and irritate the skin and respiratory tract of humans. Water Algal bloom § Dense aquatic population of microscopic photosynthetic organisms produced by an abundance of nutrient salts in surface water, coupled with adequate sunlight for photosynthesis. § The microorganisms or the toxic substances that they release may discolor the water, deplete its oxygen content, poison aquatic animals and waterfowl, and irritate the skin and respiratory tract of humans. Water blooms 65 Fungi 66  Kingdom: Fungi (Mycota) Salient Features Fungi are non chlorophyllous, eukaryotic, organisms. They are a large and successful group. They are universal in their distribution. They resemble plants in that they have cell walls. But they lack chlorophyll which is the most important attribute of plants. They are ubiquitous in habitat which ranges from aquatic to terrestrial. They grow in dark and moist habitat and on the substratum containing dead organic matter. Mushrooms, moulds and yeasts are the common fungi. The study of fungi is known as Mycology. It constitutes a branch of microbiology because many of the handling techniques used, such as sterilizing and culturing procedures are the same as those used with bacteria. Distinguishing Features of Fungi 1. They have definite cell wall made up of chitin. 2. They are without chlorophyll, hence they exhibit heterotrophic mode of nutrition. They may be saprotrophic in their mode of nutrition or parasitic or symbiotic. 3. They are usually non – motile except the subdivision Mastigomycotina. 4. Their storage product is not starch but glycogen and oil. 5. They reproduce mostly by spore formation. However sexual reproduction also takes place. Structure The body structure of fungi is unique. The somatic body of the fungus is unicelllular or multi-cellular or coenocytic. When multi-cellular it is composed of profusely branched interwoven, delicate, thread like structures called hyphae, the whole mass collectively called mycelium. The hyphae are not divided into true cells. Instead the protoplasm is either continuous or is interrupted at intervals by cross walls called septa which divide the hyphae into compartments similar to cells. Thus hyphae may be aseptate (hyphae without cross walls) or septate (hyphae with cross walls).When aseptate they are coenocytic containing many nuclei. Each hypha has a thin rigid wall, whose chief component is chitin, a nitrogen containing polysaccharide also found in the exoskeleton of arthropods. Within the cytoplasm 67 the usual eukaryotic organelles are found such as mitochondria, golgi-apparatus, endoplasmic reticulum, ribosomes and vacuoles. Nutrition Fungi are heterotrophic in their mode of nutrition that is they require an organic source of carbon. In addition they require a source of nitrogen, usually organic substances such as amino acids. The nutrition of fungi can be described as absorptive because they absorb nutrients directly from outside their bodies. This is in contrast to animals which normally ingest food and then digest it within their bodies before absorption takes place. With fungi, digestion is external using extracellular enzymes. Fungi obtain their nutrients as saprotrophs, parasites or symbionts. Saprotrophs A saprotroph is an organism that obtains its food from dead and decaying matter. It secretes enzymes on to the organic matter so that digestion is outside the organism. Soluble products of digestion are absorbed and assimilated within the body of the saprotroph. Saprotrophic fungi and bacteria constitute the decomposers and are essential in bringing about decay and recycling of nutrients. Parasites A parasite is an organism that lives in or on another organism, the host from which it obtains its food and shelter. The host usually belongs to a different species and suffers harm from the parasite. Parasites which cause diseases are called pathogens. Some parasites can survive and grow only in living cells and are called biotrophs or Obligate Parasites. Others can infect their host and bring about it’s death and then live saprotrophically on the remains, they are called necrotrophs or 68 facultative parasites. Fungal parasites may be facultative or obligate and more commonly attack plants than animals. Obligate parasites often possess specialized penetration and absorption devices called haustoria. Each haustorium is a modified hyphal outgrowth with a large surface area which pushes into living cells without breaking their plasma membrane and without killing them. Haustoria are rarely produced by facultative parasites. Symbiosis : Two important types of symbiotic union are made by fungi. Lichens and Mycorrhizae. Lichens They are symbiotic association found between algae and fungi. The alga is usually a green alga or blue green alga. The fungus is an ascomycete or basidiomycete. It is believed that the alga contributes organic food from photosynthesis and the fungus is able to absorb water and mineral salts. The fungus can also conserve water and this enables some lichens to grow in extreme dry conditions where no other plants can exist. Lichens- Blue green algae live in a Symbiotic relationship with fungi. Together, the algae and the fungus form a living unit. The algae through photosynthesis produce sugar as a food source, and the fungus provides support and protection from drying. Lichens 69 Mycorrhizae These are symbiotic associations between a fungus partner and roots of higher plants. Most terrestrial plants enter into this kind of relationship with soil fungi. The fungus may form a sheath around the center of the root (an ectotrophic mycorrhiza) or may penetrate the host tissue (an endotrophic mycorrhiza). The fungus receives carbohydrates and vitamins from the tree and in return breaks down proteins in the soil to amino acids which can be absorbed and utilized by the plant. In addition the fungus provides a greater surface area for absorption of ions such as phosphates. Figure photo in the right show the plant roots surrounded by mantle, photo in the left shows the Cross section of a root: Outer most layer is the mantle layer of mycelium. The round cells are the cortical cells and if you look closely, where the fungus mycelium is growing between the cortical cells, but not penetrating them, is the Hartig net. From Reproduction of Fungi 1. Fungi exhibit the phenomenon of alteration of generation. They have both haploid and diploid stage. 2. The main life cycle of a fungi: A. It starts with a haploid reproductive cell called spore that germinate to a single filament called hypha which grows and branches to form a mass of hyphae called mycelium that carry the fruiting body with the reproductive cells (spores). 70  The main life cycle of Fungi (Alternation of generation). B. Fungi spend most of their time as haploid (n) organisms. However, most form a temporary diploid structure for reproduction. The three following stages occur during sexual reproduction…. plasmogamy, karyogamy and meiosis. C. Plasmogamy is the fusion of two haploid cells from two separate fungi strains. D. Karyogamy is the fusing of the two haploid nuclei of a dikaryon to form a single diploid nucleus. E. Meiosis of the diploid nucleus restores the haploid number 13. Asexual reproduction includes: 1. Fragmentation: the breaking up of hypha 2. Budding: the pinching off of a small hypha outgrowth 3. Asexual spores: there’s two kinds of asexual spores 71  Fragmentation External spore Internal spores a. Sporangiospores are produced by sporangia which are located on top of a filament called a sporangiophore.(internal spores) b. Conidia are formed at the tips of specialized hyphae called conidiophores. (external spores). Major characteristics of Fungi 1. Fungi are eukaryotic organisms means they have true nucleus which are enclosed in membranes. 2. The body of fungi consists of filamentous Hyphae that can grow and form a network called a mycelium.; but a few are unicellular single celled or budding forms like yeast. 3. They reproduce by means of spores. There are sexual and asexual spores 4. Fungi exhibit the phenomenon of alteration of generation. They have both haploid and diploid stage. 5. Fungi are sedentary (non-motile) (some fungi have motile spores). 6. They lack chlorophyll. Fungi are heterotrophic organisms. They obtain its food and energy from organic substances, plant and animal matters. A. Those that obtain nutrients and energy from non-living (dead) hosts are called saprophytes (they are great recyclers) B. Those that obtain nutrients and energy from living hosts are called parasites 72  7. Most fungi are decomposers that produce powerful digestive enzymes that they introduce into their immediate environment to break down organic matter (digestion take place outside the body and absorbance of foods through cell walls). 8. The mycelium (mass of hyphae) is actually a network of filaments called hyphae. 9. There are 2 kinds of hyphae based on the morphology of cell wall: A. Septate - hyphae that are divided into successive compartments by cross walls or septa B. Coenocytic (non-septate and have many nuclei) - hyphae that are continuous and are without cross walls Fungal mycelium 10. Unlike plant cells/fungal cell walls contain chitin rather than cellulose (recall chitin is found in the exoskeleton of insects and other arthropods). 11. The energy reserve of fungi is not starch - like plants; but is glycogen - like animals. Classification of fungi The kingdom fungi mostly classified by the shape of the “Fruiting Bodies” The “Fruiting Bodies” are the reproductive structures. It is classified into 9 divisions however only four divisions will be presented in our course Zygomycetes (bread mold) 73  Basidiomycetes (mushrooms, puff balls, bracket fungi) Ascomycetes (cup - sac fungi) Deuteromycetes (Imperfect fungi) Classification of Fungi Traditionally fungi have been regarded as plants. At one time fungi were given the status of a class and together with the class algae formed the division Thallophyta of the Plant Kingdom. The thallophyta were those plants whose bodies could be described as thalli. A thallus is a body, often flat, which is not differentiated into true roots, stem and leaves and lack a true vascular system. A modification of the scheme of classification of fungi proposed by Ainsworth (1973) and adopted by Webster (1980) is outlined below. Division Myxomycota: They lack cell wall and are quite unusual organisms. they are of a slimy consistency; hence they are also called “Slime moulds”. Division Eumycota: True fungi, all with cell wall. It is customary to recognize five subdivisions under this division. A. Mastigomycotina: These are zoosporic fungi, many are solely aquatic. Three classes are included in this, each characterized by their distinctive type of zoospores. B. Zygomycetes: Vegetative body haplophase. Asexual reproduction occurs by sporangiospores. Asexual spores (sporangiospores) are non-motile spores. Sexual reproduction takes place by the complete fusion of two multi-nucleate gametangia producing a zygospore (Sexual spores) in a in zygosporangium. The common black, bread moulds Rhizopus and Mucor belong to this group. Rhizopus is a very common saprotroph similar in appearance to Mucor, but more widespread. 74 75  + Mating type (N) - Mating type C. Ascomycetes: Hyphae are septate, vegetative body is haplophase. This subdivision includes forms such as yeasts, brown moulds, green moulds, pink moulds, cup fungi, and edible morels. In this group of fungi asexual reproduction takes place by various types of nonmotile spores such as conidia. Sexual reproduction also takes place. The ascomycetes or sac fungi are characterized by the development of spores called ascospores. These ascospores are enclosed in a sac like structure, the ascus. In primitive ascomycetes the asci occur singly. In advanced ascomycetes, groups of asci get aggregated to form compact fruiting bodies called the ascocarps. The ascocarps are of three types. 1.Cleistothecium: These are closed and spherical ascocarps. eg. Eurotium 2. Perithecium: These are flask shaped ascocarps. eg. Neurospora. 3. Apothecium : These are cup shaped ascocarps. eg.Peziza. 76 D. Basidiomycetes: Hyphae are septate, vegetative body is dikaryophase. It includes the highly evolved fungi. This group got its name from the basidium, the club shaped structure formed at the tip of the reproductive hypha. Each basidium bears four basidiospores at its tip. Large reproductive structures or fruiting bodies called basidiocarps are produced in this group of fungi. Common examples for basidiomycetes include mushrooms, toadstools, puffballs and bracket fungi. 77 E. Deuteromycetes: They are the so-called “Fungi Imperfect”. It is a group of fungi known only from their asexual (imperfect or anamorphic) or mycelial state. Their sexual (perfect or teleomorphic) states are either unknown or may possibly be lacking altogether. Alternaria sp Fusarium sp Economic importance of Fungi Fungi are useful to mankind in many ways. These organisms play an important role in medicine, agriculture and industry. They have harmful effects also. Useful aspects of fungi 1) Cooking and baking (Yeast) 2) Beer and wine production Brewing and baking industries rely heavily on the uses of yeast (Saccharomyces). Yeasts ferment sugar solution into alcohol and carbon-di oxide. Alcohol is used in brewing industry and CO 2 in baking industry. 3) Cheese production 4) Production of Antibiotics The antibiotic Penicillin was discovered in 1928 by Alexander Fleming of Britain from the fungus Penicillium notatum, which in 1940s emerged as a ‘wonder drug’ for the treatment of bacterial diseases. Many other important antibiotics are 78  produced by moulds. Many fungi such as yeast, mushrooms, truffles, morels etc., are edible. Edible mushrooms contain proteins and vitamins. 5) Important agents for bioremediation (toxic waste cleanup) 6) Medical benefits (anti-cancer, anti-inflammatory) 7) Parasites and diseases in animals (ringworm, aflatoxins) 8) Parasites and diseases in plants (powdery mildew, smuts, rot) 9) Decomposition and nutrient cycling (Recycling) 10) Mycorrhizal associations: Some fungi show mutualistic relationship with roots of higher plants. Harmful aspects of Fungi Fungi are great nuisance. They grow on every thing from jam to leather and spoil them. The association of fungi with several plant diseases has now come to light. The devastating disease called ‘late blight of potato’ caused by the fungus Phytophthora infestans in Ireland in the year 1845 has resulted in such a disaster that about one million people died of starvation and over 1.5 million people fled to other countries since potato was the staple food of Ireland. Since then ‘Plant pathology’ a new science started which deals with diseases of plants caused not only by fungi but also by bacteria, viruses etc. 79  Algae gae Kingdom: Protista Plant like Protists 80  Algae General classification 81 The term Algae has no formal taxonomic standing. What are the Algae. ❖ Algae (singular alga) are an ancient group of aquatic photosynthetic organisms, which gave rise to the land plants. Nowadays, taxonomists consider other algae to be protists rather than plants. There are thought to be about 23,000 species of algae. ❖ They are autotrophic organisms and they have chlorophyll. They are O 2 producing photosynthetic organisms that have evolved in and have exploited an aquatic environment. The study of Algae is known as Algology or phycology. ❖ The names of the algal groupings used here are traditional botanical groupings which have now been overturned by modern classification systems. ❖ Kingdom Protista, otherwise called Proctotista, is the least homogenous (i.e. heterogenous) group and the hardest to define. It is something of a grab-bag containing all eukaryotes that do not fit the definitions of plants, animals and fungi. ❖ Most algae are traditionally considered as a plant subkingdom within the 5- kingdom classification. Other biologists who were convinced that not all algae are plants revised the classification, preferring algae to be placed in Kingdom Protista, with only some multicellular phyla, particularly the Chlorophyta, Rhodophyta and Phaeophyta, remaining as plants. Then there were other biologists who regarded some of these multicellular forms to be placed in Kingdom Protista. The result was, and still is confusion. 82  ❖ Occurrence and Distribution ❖ Most of the algae are aquatic either fresh water or marine. Very few are terrestrial. A few genera grow even in extreme condition like thermal springs, glaciers and snow. ❖ The free floating and free swimming minute algae are known as phytoplankton. Species that are found attached to the bottom of shallow water along the edges of seas and lakes are called Benthic. Some of the algae exhibit symbiotic association with the higher plants. Some species of algae and fungi are found in association with each other and they are called Lichens. A few species of algae are epiphytes (i.e they live on another plant or another alga) and some of them are lithophytes (i.e they grow attached to rocks). The general classification of groups within the algae (ALGAL DIVERSITY): Algae are classified according to the following characters: 1- The nature of the chlorophylls and accessory pigments present in the photosynthetic membranes. color (photosynthetic pigments) 2- Chloroplast structure. 3- The chemistry of cell walls. 4- Number and position of flagella. 5- The form of food reserves in cells (storage material). These properties are used to categories algae and assess relationships amongst them. 83 Summary of the characteristics of the traditional algal groups. Major Common Reserve Group Accesory Flagella Remarks Name food Pigment Most Chlorophytes Green algae chl b. starch (2) diverse group proeinaceou pellicle ß 1-3 instead of Euglenophytes Euglenoids chl b glucan 2 wall; facultative autotrophs ß 1-3 fucoxanthin Usually Phaeophytes Brown algae (carotenoid) glucan, (2) macro-algae mannitol Golden-brown Diatoms fucoxanthin ß 1-3 Chrysophytes algae (carotenoid) glucan (1 - 3) with SiO2 (incl. diatoms) walls floridean Usually Rhodophytes Red algae Phycoerythrin starch 0 macro-algae Internal peridinin form of Pyrrophytes Dinoflagellates (carotenoid) starch 2 cellulose wall The difference between Algae and land plants:- 1. Body plan: There is no specialization of the algal body into root, stem, leaves with vascular tissue. The photosynthetic portion of the alga is a thallus while the attachment portion comprises hair-like rhizoids. For this reason, old classification 84 systems put the algae into a grouping known as the Thallophytes (has no vascular tissue) 2. No Embryo: For most algae, sperm and eggs fuse in the open water and the zygote develops into a new plant without any protection. For other plant groups the zygote develops into an embryo within the protection of the parent plant. For this reason, old classification systems termed all other plant groups Embryophytes. 3. Reproductive structures: The gametes are produced within a single cell. There is no jacket of sterile cells protecting the gametes. *Terrestrial algae are effectively surviving in an aquatic environment on land. Soil algae survive in a film of soil-water. Different forms of algae (Thallus organization) The thalli of algae exhibit a great range of variation in structure and organization. It ranges from microscopic unicellular forms to giant seaweeds which may measure up to 100 meters long. Some of them form colonies, or filaments. The unicellular form may be motile as in Chlamydomonas or non-motile as in Chlorella. 1. Non-motile unicell – Chlorella 2. Motile unicell – Chlamydomonas 85 Colonies: They comprise single cells which typically exists as clumps. The key point about colonies is that there is no division of labour and each cell can survive on its own. Oocystis is an example of a colonial green alga. COENOBIA: The coenobium (plural coenobia) is a colony with a fixed number of cells. Coenobia may be motile or non-motile. Volvox is an example of a motile coenobium. It comprises a set number of Chlamydomonas-like cells embedded. Scenedesmus is an example of a non-motile coenobium. Typically, this coenobium comprises 4 cells. The 2 end cells have horn- like projections of their walls. COENOBIA Volvox COENOBIA Scenedesmus and Pediastrum Siphonous thallus Algae with this body are actually giant unicells. These algae are coenocytic which means they undergo repeated nuclear division without the accompanying formation of cell walls. These have a tubular structure with the multinuclear cytoplasm lining the thallus (the Greek word for tube is siphon). Bryopsis - a siphonous thallus. FILAMENTS Spirogyra is a familiar unbranched filamentous alga. It has a single spiral chloroplast in each cell. There are also other algae with branched filaments. Where there are 86 basal, prostrate filaments for attachment and erect branches for photosynthesis, this is said to be a heterotrichous filament. The chlroplasts of algae present a varied structure. For eg. they are cup Shaped in Chlamydomonas, ribbon-like in Spirogyra and star shaped in Zygnema. Bryopsis, Siphonous thallus A single cell of Spirogyra (unbranched multicellar filament) These filamentous form may be free floating or attached to a substratum. Attachment of the filament is usually effected through a simple modification of the basal cell into a holdfast. Macroscopic Algae ❖ Some of the Algae are macroscopic. eg. Sargassum, Laminaria, Fucus etc. where the plant body is large. In Macrocystis it is differentiated into root, stem and leaf like structures. ❖ Seaweeds made up of "boxy" cells like those of higher plants are termed parenchymatous. Others in cross-section appear to be parenchymatous but are in fact really made up of interwoven filaments which give this appearance! These are termed pseudoparenchymatous. They may be membranous like Ulva, the sea lettuce, or have a complex structure with a stem-like portion termed a stipe with leafy appendages as in Sargassum. 87  ❖ Ulva is a membranous sheet with a holdfast for attachment. It grows in shallow sea water, often where there is nutrient-rich run off from the land. Ulva (Sea lettuce) Reproductive diversity within the algae A- Asexual reproduction:- Algae reproduce asexually by fragmentation and by Asexual spores. In the sea, which is such a stable environment, spores are a means of dispersal not a resting stage. B- Sexual reproduction :- involves the fusion of gametes (syngamy) by male and female gametes. In algae three forms are found: 88  1. Isogamy - equal-sized motile gametes 2. Anisogamy - motile gametes almost not equal-sized 3. Oogamy - small motile male gamete, large non-motile female gamete Division: Chlorophytes ❖ These are closest to the land plants and are considered their ancestors as they share common features: - ❖ photosynthetic pigments - chlorophylls a & b, ß- carotene ❖ cell wall - cellulose-rich ❖ reserve food - starch ❖ This is a very diverse group, showing almost the full spectrum of morphological possibilities - from unicells to macroalgae. Division: Euglenophytes ❖ Euglena is probably the best-known member of this group of unicellular flagellates. These Euglen(o)ids resemble green algae in their photosynthetic pigments (chlorophylls a & b, ß-carotene) and probably got their plastids second hand from green algae. They differ in that they: *store paramylon (a 1,3 ß glucan) and fat *lack a cell wall but have a pellicle (protein plates underly the cell membrane) *can be heterotrophic (hence these organisms were once studied by zoologists!) Euglena can cause algal blooms. Euglena 89  Euglena Division: Chrysophytes (golden-brown algae) (Diatoms) ❖ Diatoms are probably the most important members of this group- responsible for 20% of global CO2 fixation. ❖ They have an outer case or frustule made of silica and are motile Diatoms Phaeophytes (brown algae) ❖ These are almost all marine macro-algae. ❖ They contain chlorophylls a & c and the brown carotenoid fucoxanthin. ❖ Their reserve, a 1,3 ß glucan called laminarin, is stored outside the plastid. 90 Some brown algae are 60 m in length. Brown algae Lamnaria Life Cycle of Fucus The conceptacles first release either antheridia or oogonia depending on the sex of the plant. The antheridia then release 64 sperm cells and the oogonia release eight eggs each. The sperm cell then fuses with an egg and fertilizes it to create a zygote. The zygote then goes through mitosis to eventually turn into a small bladder wrack and then the organism eventually grows into sexual maturity with the signature pairs of bladders, and the cycle then repeats itself every year. Alternation of generation life cycle 91 Division :Dinophyta ❖ Unicellular ❖ Contain two flagella ❖ Most have disc-shaped chloroplasts ❖ Contain xanthophyll pigments. ❖ Many have tiny projectiles. ❖ Many types of toxins produced. Human and ecological relevance These produce red tide, produce powerful neurotoxins that accumulate in shellfish. About 2000 people become ill each year, with 15% fatally from eating contaminated shellfish. Division: Rhodophyta (Red Algae) ❖ Most species are seaweed. ❖ Tend to occur in warmer and deeper waters than brown algae. ❖ Most are filamentous. ❖ Relatively complex life cycle involving three types of thallus structures. 92  ❖ Colors mostly due to phycobilins. ❖ Numbers of species produce agar. Polysiphonia ❖ Dense tuft , 10cm or more ❖ Colour: brownish-red to dark purple-red ❖ Plant body: ❖ Basal prostrate filaments ❖ Erect or vertical filaments ❖ Main axis: uniaxial and ❖ Multiaxial in adult portion (siphons) ❖ Male reproductive organ called spermatangium or antheridium ❖ Female reproductive organ called carpogonium 93