Taxonomy, Systematics and Classification of Microorganisms PDF

Taxonomy, Systematics and Classification of Microorganisms Molecular Biology and Biotechnology, Genetics, and Microbiology Division, Institute of Biological Sciences, Central Mindanao University Notice: This material is provided to you as study material/guide in Bio 43 (General M...

Taxonomy, Systematics and Classification of Microorganisms Molecular Biology and Biotechnology, Genetics, and Microbiology Division, Institute of Biological Sciences, Central Mindanao University Notice: This material is provided to you as study material/guide in Bio 43 (General Microbiology). You are not permitted to share this material either in electronic or printed forms including uploading it in the public databases. Modern world : enormous diversity of life forms (including microorganisms) ~ 30,000 bacterial species formally named. There are 1 trillion estimated microbial species. However, 99.99% of them are still The diversity of life undiscovered! © Cold Spring Harbor Lab Why such great diversity? Biological Evolution Earth’s age now : 4.6 B years old. What were the conditions of the primitive Earth? Anoxic and reducing environment (more of CH4, CO2, N2, NH3, H2S, FeS). Hotter (> 100 °C); with frequent volcanic activity. With strong radiation. Depiction of the early Earth. © Smithsonian magazine. © Pearson Education 2019. Brock Biology of Microorganisms.  What was the first life forms? May have been self-replicating RNAs. © Pearson Education 2019. Brock Biology of Microorganisms.  Gradual changes from an anoxic to oxic Earliest prokaryotes environment. ▪ likely to be Enormous burst in the rate of evolution anoxygenic phototrophic Aerobic organisms evolved bacteria. ▪ Evolution of oxygenic Appearance of eukaryotic microorganisms photosynthesis in the Diversification of metazoa (multicellular cyanobacteria ~ 3 organisms) BYA. Gradual changes from an anoxic to oxic environment. Evolution of a greater diversity of life forms Microbial Diversity Arose a result of evolution: by mutation and genetic recombination. The need for taxonomy and systematics – to give sense of the present diversity. Carolus Linnaeus – Father of Taxonomy. Two important contributions: 1. Hierarchical classification system. 2. The system of binomial nomenclature (naming). Classification Systems: Two-Kingdom – Animalia and Plantae ( by C. Linnaeus, 1758). Three-Kingdom – Animalia, Plantae, and Protista (by Ernst Haeckel, 1860). Five- Kingdom – Animalia, Plantae, Fungi, Protista, and Monera (by R.H. Whittaker, 1969). Six-Kingdom – Animalia, Plantae, Fungi, Protista, Eubacteria, and Archaebacteria (Carl Woese, 1977) Seven-Kingdom – Animalia, Plantae, Fungi, Protozoa, Chromista, Eubacteria, and Archaebacteria (Thomas-Cavalier Smith, 1987). Three-Domain – Eukarya, Archaea, Eubacteria (Carl Woese, 1990). History of Bacterial Systematics: Four Phases Phase of ”early descriptions” on morphology (1872- 1900). Description of bacterial physiology and ecology (1900-1955). Description of chemical structures of cell constituents (Chemotaxonomy) (1955-1980). Use of DNA techniques (1980-present). Definition of Terms: Taxonomy The science of biological classification. - describing, identifying, classifying, and naming of organisms Chapter 5. Classification of Microorganisms 10 Classification Grouping organisms into taxa based on mutual similarity or evolutionary relatedness. Chapter 5. Classification of Microorganisms 11 Identification Characterization of an isolate to determine what species it is. Chapter 5. Classification of Microorganisms 13 Nomenclature Assignment of names to taxonomic groups in agreement with published rules. International Code of Nomenclature of Prokaryotes (Prokaryotic Code) Chapter 5. Classification of Microorganisms 14 Systematics Study of the diversity of life (both past and present) and the relationships among living things through time - uses taxonomy as a means to understand organisms Chapter 5. Classification of Microorganisms 15 Species (in prokaryotes) collection of strains that share many stable properties in common and differ significantly from other group of strains. Species (in eukaryotes) - a group of closely related organisms that breed among themselves. 16 Strain population of organisms that descends from a pure culture isolate or from a species. eg., E. coli O157:H7 vs E. coli O111 Chapter 5. Classification of Microorganisms 17  Classification Artificial Classification Based upon the expressed characteristics or the phenotype of the organism. Chapter 5. Classification of Microorganisms 18  Classification Natural or Phylogenetic Classification Based upon the suggested evolution of the organism. i.e., those that share a common ancestor Chapter 5. Classification of Microorganisms 19 Five Kingdoms Mode of nutrition Uni-/multicellular Robert Whittaker (1969) Chapter 5. Classification of Microorganisms 20 Six Kingdoms Carl Woese (1977) Three Domains Carl Woese in 1990 differences in 16S rRNA gene sequence Chapter 5. Classification of Microorganisms 23 Summary of the proposed classification schemes  Nomenclature Principles: ▪ Each distinct kind of organism is designated as a species. List of species of prokaryotes Bergey’s Manual of Systematic Bacteriology Chapter 5. Classification of Microorganisms 25 Nomenclature Principles: Carl Linnaeus ▪ The species is designated by a Latin binomial to provide a characteristic international label.  Binomial System (Carl von Linnè/Carolus Linnaeus) ▪ Each organism is placed in a genus and given a species name Escherichia coli Escherichia coli  ▪ Names are descriptive Diplococcus salivarius Staphylococcus aureus (Greek Staphyle, “bunch of grapes”, kokkos “berry”, Latin aurum “gold) Thiomargarita namibiensis Sulfur Pearl of Namibia Caldivirga maquilingensis Mud Spring Mt. Maquiling, Laguna Philippines Caldisphaera lagunensis  Nomenclature Principles: ▪ The application of names is regulated. ▪ A law of priority ensures the use of the oldest available legitimate name. Chapter 5. Classification of Microorganisms 31  Nomenclature Principles: Generic Name: can change if the organism is assigned to another genus because of new information. Specific Name: stable; the oldest epithet for a particular organism takes precedence and must be used. Pseudomonas solanacearum Ralstonia solanacearum Pseudomonas cepacia Burkholderia cepacia Aquaspirillum magnetotacticum Magnetospirillum magnetotacticum  Nomenclature Principles: ▪ Designation of categories is required for classification of organism. Taxon = group Taxa = groups Chapter 5. Classification of Microorganisms 35  Nomenclature Principles: ▪ Criteria are established for effective publication of new specific names, as well as guidance for forthcoming new names. Chapter 5. Classification of Microorganisms 36  Nomenclature Rules for naming bacteria International Code for the Nomenclature of Bacteria (1991) Questions on nomenclature International Journal of Systematic Bacteriology (IJSB) Chapter 5. Classification of Microorganisms 37 International Code of Nomenclature of Prokaryotes (Prokaryotic Code) Published by the International Journal of Systematic and Evolutionary Biology (IJSEM). Revised in 2022. Provides guidelines and rules in naming new species. Examples of guidelines for nomenclature (from the Prokaryotic Code): Principle 1. The essential points in nomenclature are to: Aim at stability of names; Avoid or reject the names that cause error or confusion; Avoid the useless creation of names; Nothing in this Code may restrict the freedom of taxonomic thought or action.  Principle 2. The nomenclature of prokaryotes is not independent of botanical and zoological nomenclature. When naming new taxa in the rank of genus or higher, due consideration is to be given to avoiding names which are regulated by the International Code of Zoological Nomenclature and the International Code of Nomenclature for algae, fungi and plants. Principle 3. The names of all taxa are Latin or latinized words treated as Latin, regardless of their origin. They are usually taken from Latin or Greek. Principle 4. The purpose of giving a name to a taxon is to supply a means of referring to it rather than to indicate the characters or the history of the taxon. Principle 5. The application of the names of taxa is determined by means of nomenclatural types, referred to in this Code as types.  Principle 6. The correct name of a taxon is based upon valid publication, legitimacy and priority of publication. Principle 7. A name of a taxon has no status under the Rules and no claim to recognition unless it is validly published. Principle 8. Each phylum or taxon of a lower rank with a given circumscription, position, and rank can bear only one correct name, i.e., the earliest that is in accordance with the Rules of this Code. Provision has been made for exceptions to this Principle. Principle 9. The name of a taxon should not be changed without sufficient reason; if necessary, changes should be based upon further taxonomic studies or on the necessity of expunging a name that is contrary to the Rules of this Code.  Characterization and Identification Involves the study, not of a single cell, but of a population of identical cells Prerequisite: pure culture Chapter 5. Classification of Microorganisms 42  Reasons for doing characterization identification purposes comparison with other organisms exploit characteristics which may be beneficial Major Characteristics Used in Taxonomy 1 Cultural 2 Morphological 3 Metabolic 4 Chemical Composition 5 Antigenic 6 Genetic  1 Cultural refer to the nutrients required for growth and the physical conditions of an environment that will favor growth. 1 Cultural Based on Energy source Nutritional Based on Carbon source types Based on C and E source Chapter 5. Classification of Microorganisms 46 1 Cultural Nutritional types Based on E source Phototrophs Chemotrophs Chapter 5. Classification of Microorganisms 47 1 Cultural Nutritional types Based on C source Autotroph Heterotroph (organotroph) Chapter 5. Classification of Microorganisms 48 1 Cultural Nutritional types Based on E & C source photoautotroph photoheterotroph chemoautotroph chemoheterotroph 49 Nutritional types Carbon Type Energy Source Source Photoautotroph Sunlight CO2 Photoheterotroph Sunlight Organic compounds Chemoautotroph Inorganic chemicals CO2 (H2, NH3, NO2-, Fe2+, H2S) Chemoheterotroph Organic compounds Organic (sugars, amino acids, compounds etc) 1 Cultural temperature requirement based on physical pH requirement conditions oxygen requirement Chapter 5. Classification of Microorganisms 51 1 Cultural based on physical conditions Temperature requirement Psychrophile: between -5 and 15oC Mesophile: between 25 and 45oC Thermophile: between 45 and 70oC Chapter 5. Classification of Microorganisms 52 P Temperature requirement Psychrotroph: between 20 and 30oC, (but grows well at lower temperatures) Hyperthermophile: between 70 and 110oC 1 Cultural based on physical conditions pH requirement Acidophile optimum pH below 5.5 Neutrophile optimum pH 5-8 Alkalophile optimum pH above 8.5 54 1 Cultural based on physical conditions Oxygen requirement Aerobe strict/obligate aerobe microaerophile Anaerobe strict/obligate anaerobe facultative anaerobe aerotolerant anaerobe 1 Cultural other examples of cultural characteristics type of growth on agar media Chapter 5. Classification of Microorganisms 56 1 Cultural other examples of cultural characteristics type of growth in liquid media (ring, pellicle, flocculent) salt tolerance/requirement (halotolerant, halophile) Chapter 5. Classification of Microorganisms 58 2 Morphological Size Chapter 5. Classification of Microorganisms 59 2 Morphological Shape Stella Haloarcula 2 Morphological Arrangement 2 Morphological Structures A variety of bacterial inclusions. a. PHB granules; b. a parasporal BT crystal in the sporangium of Bacillus thuringiensis; c. carboxysomes in Anabaena viriabilis, showing their polyhedral shape; d. sulfur globules in the cytoplasm of Beggiatoa 3 Metabolic - biochemical/ physiological characteristics ie., presence of enzymes fermentation of sugar 4 Chemical Composition cell wall chemistry Gram + Gram - 4 Chemical Composition Gram reaction 4 Chemical Composition cell membrane chemistry 4 Chemical Composition capsule chemistry, etc 5 Antigenic Antigen molecule capable of inducing an immune response on the part of the host organism 5 Antigenic 5 Antigenic 5 Antigenic Chapter 5. Classification of Microorganisms 78 6 Genetic 6 Genetic DNA composition analysis, detection of the likeness or homology between DNA of cells. The Bergey’s Manual of Determinative Bacteriology A guide in identifying unknown bacteria using morphological and biochemical traits. Prepared by David Hendricks Bergey in 1993. There are nine editions. Replaced with Bergey’s Manual of Systematic of Archaea and Bacteria. Current status of bacterial taxonomy What tests or results required to identify a bacterium as a unique species? Polyphasic taxonomy- A consensus type of taxonomy; takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. Workflow of genotypic methods used in culture-dependent techniques for prokaryotic taxonomy. (Raina et al., 2019) What is a bacterial species? a group of strains that are characterized by a certain degree of phenotypic consistency, showing 70% of DNA–DNA binding and over 97% of 16S ribosomal RNA (rRNA) gene-sequence identity. Phenotype + genotype data = must agree Why identify and classify microorganisms? Determine biodiversity. Study the functions/roles of microbial species. Species – a basic taxonomic unit. What is a species? (recall the species concept). Definition of prokaryotic species: “a group of strains that are characterized by a certain degree of phenotypic consistency, showing 70% of DNA–DNA binding and over 97% of 16S ribosomal RNA (rRNA) gene-sequence identity” (Gevers et al., 2005). Entails Polyphasic Taxonomy. Prokaryotic classification Polyphasic Taxonomy A consensus type of taxonomy; no rules. it considers all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis (Vandamme, 1996).  Genotypic data Phenotypic General data phylogeny Polyphasic Taxonomy Phenotypic data Cell wall composition (Gram-negative vs. Gram-positive). Cellular fatty acids. Isoprenoid quinones. Polyamines. Total cellular proteins. Sample workflow of phenotypic methods Genotypic data DNA base ratios (mol % G+C). (same species < 3% variation; same genus < 10% variation). rRNA gene sequencing (sequence similarity of 16s rRNA sequence = > 97%, same species). DNA-DNA reassociation (same species > 70% hybridization). Conserved gene sequence analysis (genes other than 16s rRNA, i.e. rpoA, rpoB, rpoC, etc.). DNA fingerprinting (REP, BOX, ERIC PCR). Multilocus Sequence Typing. (allelic profiling). In silico phenotyping- predicting phenotypes based on genome sequences. Sample workflow for genotypic methods Describing and Reporting a New Species/Taxon Key information: Genome sequences of the type strains of prokaryotes. 16S rRNA gene sequence. Isolation, habitat, and sample description. Morphology and growth conditions. Physiology. Chemotaxonomy. Species description (Protologue). Publication in the International Journal of Systematic and Evolutionary Microbiology. Submission of pure cultures in two international culture collections.