Microbial Taxonomy PDF

MICROBIAL TAXONOMY SHAIRA DAWN G. OAQUERA FACULTY DEPARTMENT OF BIOLOGICAL SCIENCES Early Earth and Its Origin Earth formed about 4.5 billion years ago: characterized by a molten surface under intense bombardment by asteroids and other objec...

MICROBIAL TAXONOMY SHAIRA DAWN G. OAQUERA FACULTY DEPARTMENT OF BIOLOGICAL SCIENCES Early Earth and Its Origin Earth formed about 4.5 billion years ago: characterized by a molten surface under intense bombardment by asteroids and other objects from space Water on Earth originated from volcanoes, icy comets, and asteroids Water would have been present only as water vapor Sterile planet  The oldest known sedimentary rocks date to 3.86 billion years ago, indicating that oceans were present at the time these rocks formed. Stromatolites are fossilized microbial mats consisting of layers filamentous prokaryotes and trapped sediment. Hydrothermal Vent Theory conditions would have been less hostile and more stable than on Earth’s surface A steady and abundant supply of hydrogen (H2) and hydrogen sulfide (H2S) can support the abiotic production of molecules critical for the emergence of life (e.g. Amino acids, lipids, sugars, and nucleotide bases) Prebiotic chemistry -> first replicating systems (precursors to cellular life) RNA World: first self-replicating systems Component of Replaced More stable Formed with cofactors and catalytic than RNA, the early Possessed point at which Bacteria and molecules found in role of RNAs therefore a earth’s the three- Archaea became distinct and all cells, possess better conditions part and diverged and life began to catalytic activity repository of membrane diversify and catalyze protein genetic synthesis. information system  METABOLIC DIVERSIFICATION Earth was anoxic. CO2 may have been the major source of carbon for cells H2 was a major fuel for the energy metabolism of early cells Chemolithotrophic metabolism has supported the production of large amounts of organic compounds. Organic materials accumulated and provided the conditions needed for the evolution of new chemoorganotrophic bacteria.  Photosynthesis and Oxidation of Earth The metabolism of cyanobacteria yielded O2 that oxidized reduced minerals containing Ferrous ion (Fe2+) to iron oxides containing Ferric ion (Fe3+). Banded iron formations: laminated sedimentary rocks formed in iron- and silica-rich deposits. O2 begin to accumulate in the atmosphere after the abundant Fe2+ was oxidized by Iron oxides cyanobacterial photosynthesis. Atmospheric O2 reached present-day levels (~ 21%), 600-900 million years ago. As O2 accumulated on Earth, the atmosphere gradually changed from anoxic to OXIC  Ultraviolet (UV) radiation is lethal to cells and can cause severe DNA damage The Ozone When O2 is subject to UV radiation Shield from the sun, it is converted to ozone, which strongly absorbs UV radiation in wavelengths up to 300 nm Organisms could range over the terrestrial surface of Earth, exploiting new habitats and evolving ever-greater diversity.  Universal Tree of Life Depicts the evolutionary history of all cells Clearly reveals the three- domain concept Root: all extant life shared a common ancestor, the LUCA. First living things were microorganisms, the dominant life form Eukarya show greater sequence similarity to those of Archaea than to those of Bacteria.  The Three-Domain System Domain Bacteria: Domain Archaea: pathogenic, prokaryotes that do nonpathogenic, and not have photoautotrophic peptidoglycan in prokaryotes, their cell walls and live in extreme environments Domain Eukarya: Kingdom of animals, plants, and fungi Endosymbiotic Hypothesis eukaryotic nucleus probably arose as a necessity for ensuring orderly partitioning of DNA. Mitochondrion: arose from the engulfment of a bacterium capable of aerobic respiration into the cytoplasm of early eukaryotic cell Chloroplast: arose from the stable incorporation of cyanobacterium-like cell into the cytoplasm of a eukaryotic cell  Microbial Taxonomy TAXONOMY science of biological classification organisms are characterized, named, and classified according to defined criteria Consist of three separate but interrelated parts Classification the organization of organisms into groups based on either phenotypic similarity or evolutionary relationship. arrangement of organisms into groups (taxa/taxon) Nomenclature the actual naming of organisms and follows the binomial system of nomenclature assignment of names to taxa Identification determination of taxon to which an isolate belongs  Methods of Classifying and Identifying Microorganisms Taxonomy uses three kinds of methods for the identification and description of bacteria: 1. PHENOTYPIC – groups of organisms together based on mutual similarity of phenotypes  examines the morphological, metabolic, physiological, and chemical characteristics of the cell.  can reveal evolutionary relationships, but not dependent on phylogenetic analysis  Ex: Motility and Flagella Colony Morphology Cell Morphology  Cell Wall Component Gram-negative Gram-positive bacteria bacteria Methods of Classifying and Identifying Microorganisms Microbiologists have developed a variety of methods to test metabolic reactions and other characteristics to identify prokaryotes. Bergey’s Manual of Determinative Bacteriology (1923): does not classify bacteria according to evolutionary relatedness provides identification (determinative) schemes based on such criteria: cell wall composition morphology differential staining oxygen requirements biochemical testing Methods of Classifying and Identifying Microorganisms The basic taxonomic group in microbial taxonomy is the species.  Prokaryotic species: a collection of strains that share many stable properties and differ significantly from other groups of strains a collection of organisms that share the same sequences in their core housekeeping genes (required to code for products needed by the cells) – based on sequence data. Methods of Classifying and Identifying Microorganisms  Strains: descended from a single, pure microbial culture Biovars – differ biochemically and physiologically Morphovars – differ morphologically Serovars – differ in antigenic properties  Genus: a well-defined group of one or more strains clearly separate from other genera Taxonomic Hierarchy  Binomial System Homo sapiens The genus of Nomenclature means man; the specific Devised by Carolus Linnaeus epithet Every organism is assigned two names means wise. or a binomial: genus name and specific epithet (species) both names are printed underlined or italicized. Rhizopus stolonifer Genus name is always Rhizo- (root) CAPITALIZED and is always a noun. describes rootlike Species name is lowercase and is structures on the usually an adjective. fungus; stolo- (a International Journal of Systematic shoot) describes and Evolutionary Microbiology the long hyphae Methods of Classifying and Identifying Microorganisms Taxonomy uses three kinds of methods for the identification and description of bacteria: 2. GENOTYPIC:  an alternative or complement to established phenotypic methods  considers characteristics of the genome  involves the use of conserved sequences within phylogenetically informative genetic targets, such as the SSU (small subunit) rRNA gene (16S, 18S), LSU (large subunit), ITS (internal transcribed spacer) Molecular Analysis  Polymerase Chain Reaction rapidly producing millions to billions of copies of a specific segment of DNA. The DNA template contains the target sequence of DNA for copying. Primers are short oligonucleotides of DNA, usually around 20 base pairs in length. Sequence Alignment Purpose: to add gaps to molecular sequences in order to establish positional homology:  genes that have been inherited from a common ancestor Methods of Classifying and Identifying Microorganisms Taxonomy uses three kinds of methods for the identification and description of bacteria: 3. PHYLOGENETIC:  seeks to place organisms within an evolutionary framework using molecular sequence data.  Based on a direct comparison of genetic material and gene products  Phylogenetic trees: diagrams that depict evolutionary history composed of nodes and branches The tips of the branches represent species that exist today. Phylogenetic trees can be constructed that are either rooted trees or unrooted trees Phylogenetic Analysis The tips of the branches are species (or strains). Rooted tree depicts ancestral relationships. Unrooted trees depict the relative relationships among the organisms. The nodes represent a past stage of evolution where an ancestor diverged into two new lineages. The branch length represents the number of changes that have occurred. THANK YOU FOR LISTENING! 