Biodiversity Definition & Types PDF

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 biodiv...

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