Taxonomy: Classification of Organisms PDF

**TAXONOMY** is the science of organismal classification. **Classification** is the assignment of organisms (species) into an organized scheme of naming. Ideally, these schemes are based on evolutionary relationships (i.e., the more similar the name, the closer the evolutionary relationships). [Th...

**TAXONOMY** is the science of organismal classification. **Classification** is the assignment of organisms (species) into an organized scheme of naming. Ideally, these schemes are based on evolutionary relationships (i.e., the more similar the name, the closer the evolutionary relationships). [Thus, classification is concerned with: -] 1\. The establishment of criteria for identifying organisms & assignment to groups (what belongs where) 2\. The arrangement of organisms into groups of organism (e.g. At what level of diversity should a single genus be split into two or more species?). 3\. Consideration of how evolution resulted in the formation these groups. TAXON: - A group or category of related organisms. Two key characteristics of taxa are: -Members of lower-level taxa (e.g., Species) are more similar to each other than are members of higher-level taxa (e.g., Kingdom or domain). -Members of specific taxa are more similar to each other than any are to members of different specific taxa found at the same hierarchical level (e.g. Humans are more similar to apes, i.e., comparison between species, than either is similar to, for example, Escherichia coli). Thus, once you know that two individuals are members of the same taxon, you can infer certain similarities between the two organisms. NOTE that taxa are dynamic, changing as our knowledge of organisms and evolutionary relationships change **[BINOMIAL NOMENCLATURE]** \- Organisms are named using binomial nomenclature (viruses are exceptions) \- Binomial nomenclature employs the names of the two-level taxa, genus, and species, to name a species. **Binomial nomenclature includes:** i\. Genus comes before species (e.g., ***Escherichia*** *coli*) ii\. The first letter in genus name is always capitalized (e.g., **E**scherichia) iii\. Species name is never capitalized (e.g., **coli**) iv\. Both names are always either [italicized or underlined] (e.g *Escherichia coli*) v\. The genus name may be used alone, but not the species name (i.e. saying or writing "*Escherichia* "alone is legitimate while saying or writing "coli" is not) **Strain** a\) A strain, in some ways, is equivalent to a breed or subspecies among plants or animals. Strain is the level below the species b\) Two members of the same strain are more similar to each other than either is to an individual that is a member of a different strain, even if all three organisms are members of the same species **Three-domain system (Carl Woese's Classification)** The three-domain system was first introduced by **Carl Woese in 1990 . That is why it'**s called Carl Woese's Classification**.** This classification system also is known as the **Six Kingdoms and Three Domains Classification** because it divides the life forms into **three domains** and **six kingdoms**. The three domains of Carl Woese's Classification system include archaea, bacteria, eukaryotes, and the six kingdoms are Archaebacteria (ancient bacteria), Eubacteria (true bacteria), Protista, Fungi, Plantae, Animalia. This classification system divides the life based on the differences in the **16S ribosomal RNA (rRNA) structure **and as well as the cell's membrane lipid structure and its sensitivity to antibiotics. The main difference from earlier classification systems is the splitting of archaea from bacteria. The evaluating rRNA structure is very helpful. As a result of rRNA molecules, throughout nature perform the identical function, and their structure modifications very little over time. Subsequently, similarities and dissimilarities in rRNA nucleotide sequences are a very good indication of how associated or unrelated completely different cells and organisms are. **In this classification, Carl Woese uses 16S ribosomal RNA (rRNA) as a 'Chronometer', because of;** - It is universally distributed, which means it is present in all species. - It is functionally similar in all organisms. - It can change its sequence slowly. - Its sequences can be aligned or matched up between 2 organisms. **Domains of Carl Woese's Classification** Carl Woese's Classification is made of three domains such as 1. Domain Archaea 2. Domain Bacteria 3. Domain Eukarya **[1. Domain Archaea]** The Archaea domain includes all prokaryotic cells; they lack nuclear membrane, have distinct biochemistry, and contain RNA markers from bacterial cells. The Archaea are considered the oldest species of organisms on Earth. They can survive in extreme, harsh environments that differentiate them from other domains. The cell wall of archaea lacks peptidoglycan. Archae also contain ether linkages in their membranes. Archae has three phyla such as; - **Crenarchaeota:** They can survive at extremely high temperatures and extremely low temperatures. - **Euryarchaeota:** Some of them are known as extremely halophiles, which can prevent inhibit highly saline environments. - **Konarchaeota**: It includes all those species were found in a single hot spring, Obsidian Pool, present in Yellowstone National Park (USA). **[2. Domain Bacteria]** These are also prokaryotic cells with bacterial rRNA and contain diacyl glycerol diester lipids in their membrane. They are also called eubacteria or "true bacteria". Their cell membrane contains ester linkage between unbranched fatty acid chains and glycerol. Their cell wall made up of peptidoglycan. There are present 5 phyla of the bacterial domain such as; - **Proteobacteria:** The example of proteobacteria is *E. coli, Salmonella typhus, Legionella, Heliobacter pylori* (cause of many ulcers), *Neisseria gonorrhea* (cause of gonorrhea). - **Cyanobacteria: **The example of Cyanobacteria is Photosynthetic 'blue-green' bacteria which produces O2 gas. - **Eubacteria:** The example of Eubacteria is  *Clostridium* (tetanus, botulism), *Bacillus*, *Mycoplasma* (walking pneumonia). - **Chlamydias: **The example of Chlamydias is *Giardia, Chlamydia* (STD), etc. - **Spirochaetes: **The example of Spirochaetes is Spiral bacteria that cause syphilis, Lyme disease. **[3. Domain Eukarya]** These are eukaryotic cells with a membrane-bound nucleus. Their membranes contain their membranes between unbranched [[fatty acid]](https://microbenotes.com/fatty-acids/) chains and glycerol. They lack peptidoglycans on their cell wall. Eukarya inhibit the antibacterial antibiotics but sensitive to antibiotics that affect eukaryotic cells. There are presently four Kingdoms of Eukarya such as; - **Protista:** These are slime molds, euglenoids, algae, and protozoans. - **Fungi: **These are sac fungi, club fungi, yeasts, and molds. - **Plantae: **These are mosses, ferns, conifers, and flowering plants. - **Animalia: **These are sponges, worms, insects, and vertebrates. **Five Kingdom System of Classification** - Taxonomy refers to the science of classification of living organisms. - According to Bergey's Manual of Systematic Bacteriology, taxonomy consists of three separate but interrelated areas: classification, nomenclature, and identification. - Classification is the arrangement of organisms into taxonomic groups known as taxa on the basis of similarities or relationships. - Taxa include kingdoms or domains, divisions or phyla, classes, orders, families, genera, and species. - Closely related organisms (i.e., organisms having similar characteristics) are placed into the same taxon. - Organisms are categorized into larger groups based on their similarities and differences. - It should be noted that the classification of living organisms is a complex and controversial subject.  **The Five Kingdom System of Classification** - Very early on, scientists began grouping living organisms under different categories. - Some biologists classified organisms into plants and animals. - Ernst Haeckel, Robert Whittaker, and Carl Woese are some biologists who attempted a broader system of classification. - Amongst these, the Five Kingdom Classification proposed by Robert Whittaker stood out and is widely used. - In 1969, Robert H. Whittaker proposed a Five- Kingdom System of Classification, in which all organisms are placed into five kingdoms. **Features of the Five Kingdom System of Classification** Whitaker proposed that organisms should be broadly divided into kingdoms based on certain characteristics like the structure of the cell, mode of nutrition, the source of nutrition, interrelationship, body organization, and reproduction. The kingdoms include: - Bacteria and archaea are in the **Kingdom Monera** - Algae and protozoa are in the **Kingdom Protista** (organisms in this kingdom are referred to as protists) - Fungi are in the **Kingdom Fungi** - Plants are in the **Kingdom Plantae** - Animals are in the **Kingdom Animalia** **Kingdom Monera** - These organisms are prokaryotic and unicellular. - They do not have a well-defined nucleus and also lack cell organelles.   - Some organisms show the presence of cell wall while there are others without a cell wall. Consequently, some organisms are autotrophic and others are heterotrophic. - Examples include Bacteria, Cyanobacteria, and Mycoplasma. **Kingdom Protista** - Organisms grouped under Kingdom Protista are all unicellular, but eukaryotic organisms. - These are the simplest forms of eukaryotes that exhibit either autotrophic or heterotrophic mode of nutrition. - Some organisms have appendages such as cilia or flagella or pseudopodia to move around. - Some examples are Diatoms, Protozoans like Amoeba, Paramecium **Kingdom Fungi** - Heterotrophic, Multicellular and Eukaryotic organisms are grouped under Kingdom Fungi. - Their mode of nutrition is saprophytic as they use decaying organic matter as food. - They have cell walls, which are made up of a substance called Chitin. - Fungi also form a symbiotic association with some blue-green algae.  - Yeast, Mushroom, Aspergillus are examples of Fungi. **Kingdom Plantae** - These are Eukaryotic, Multicellular organisms with a cell wall that is made up of cellulose. - They are autotrophs and synthesize their own food through the process of photosynthesis. This kingdom includes all plants. - Based on the body differentiation and presence or absence of specialized vascular tissue, Kingdom Plantae is divided into different divisions, namely Thallophyta, Bryophyta, Pteridophyta, Gymnosperms, and Angiosperms. - Examples are Spirogyra, Ferns, Pines, and Mango Plant etc. **Kingdom Animalia** - This Kingdom includes organisms that are Multicellular, Eukaryotic, without the presence of cell wall. - They have a heterotrophic mode of nutrition. - They also exhibit great diversity. Some organisms are simple while others have a complex body with specialized tissue differentiation and body organs. - The Animal Kingdom is divided into many phyla and classes. - Some of the phyla are Porifera, Coelenterata, Arthropoda, Echinodermata, Chordata etc. Examples -- Hydra, Starfish, Earthworms, Monkeys, Birds etc. - Viruses are not included in the Five-Kingdom System of Classification because they are not living cells; they are acellular. - Four of the five kingdoms consist of eukaryotic organisms. - Each kingdom consists of divisions or phyla, which, in turn, are divided into classes, orders, families, genera, and species. - In some cases, species are subdivided into subspecies, their names consisting of a genus, a specific epithet, and a subspecific epithet (abbreviated "ssp.") An example would be *H. influenzae* ssp. *aegyptius*, the most common cause of "pinkeye." - Although Whittaker's Five-Kingdom System of Classification has been a popular classification system for the past 30 or so years, not all scientists agree with it and other taxonomic classification schemes exist. **[Viral classification]** Classification of viruses is not nearly as well developed as the classification of cellular organisms. Today viruses tend to be classified by their chemical, morphological and physiological attributes (e.g. genome = DNA vs RNA, virion particle = enveloped vs non enveloped and myriad details of their intracellular infection cycles). Binomial nomenclature is not employed to name viruses; instead viruses are named by their common names (e.g., Human Immunodeficiency Virus a.k.a HIV) **Limitations or Objections to the Five Kingdom System of Classification** - Some scientists do not agree that algae and protozoa should be placed into the same kingdom. - In some classification schemes, protozoa are placed into a subkingdom of the Animal Kingdom. - A distinction between unicellular and multicellular organisms is not possible in case of algae in this system of classification. - Each group has so many diversities that it is difficult to keep them together. For example, monera and Protista contain both walled and wall-less organisms. Photosynthetic and non-photosynthetic organisms, cellular or filamentous organism. - Virus has not been included in this kingdom. - Archaebacteria differ from other bacteria in structure, composition and physiology. - Mycoplasma are quite different form bacteria where they have been placed along with prokaryotes. - Symbiotic associations are not considered in this classification system. For example, lichens are organisms which are formed by the symbiotic association between fungi and algae. **[Dichotomous key]** A means of assigning an organism to a specific taxonomic category typically involves the use of specific criteria that may posed as questions (e.g. What does the organism look like etc.). Relevant criteria may be arranged as a dichotomous key. In a dichotomous key questions are arranges hierarchically with more general questions are asked first, with questions becoming more specific asked subsequently. **[EUKARYOTIC CELL]** Eu- true Karyote- nucleus The eukaryotic cell has a true membrane bound nucleus, usually containing multiple chromosomes, a mitotic apparatus, a well-defined endoplasmic reticulum and mitochondria. **PROKARYOTIC CELL** Pro- primitive Karyote- nucleus The prokaryotic cell possesses naked DNA without associated basic proteins, divides amitotically by binary fission and bounded by a semi rigid cell wall. The distinguishing features between Eukaryotic cell and Prokaryotic cell **Features** **Prokaryotic Cell** **Eukaryotic Cell** --------------------------------------- ---------------------------- ---------------------------- **Size** Small about 1 μm Variable upto 10 μm **Nuclear membrane** Absent Present **Genetic material** Single circular DNA Linear multiple chromosome **Nucleolus** Absent Present **Histones** Absent Present **Sexual reproduction** Absent Present **Ribosome** 70s 80s **Mitochondria** Absent Present **Endoplasmic reticulum** Absent Present **Lysosomes** Absent Present **Micro filaments and tubules** Absent Present **Site of oxidative phosphorylation** Cell membrane Mitochondria **Site of photosynthesis** Cell membrane Chloroplast **Peptidoglycan** Present Absent **Cell membrane composition** Phospholipids and Proteins Sterols **Genes** No Introns Presence of Introns **[Bacterial Cell]** General property: Typical prokaryotic cell Contain both DNA and RNA Most grow in artificial media Replicate by binary fission Almost all contain rigid cell wall Sensitive to antimicrobial agent