Lecture 2. Bacteriology II. PDF

Microbial diversity and evolution Learning outcomes Gain an understanding of the use of phylogeny in classification. Understand the main characteristics of different groups of microorganisms. Consider the role of mutation in the development of resistance and evolution of bacteria. Ta...

Microbial diversity and evolution Learning outcomes Gain an understanding of the use of phylogeny in classification. Understand the main characteristics of different groups of microorganisms. Consider the role of mutation in the development of resistance and evolution of bacteria. Taxonomy vs phylogeny Taxonomy: Science of Phylogeny: Comparative biological classification. analysis of an organism on Includes classification, the basis of evolutionary nomenclature and relationships. identification. Carl Linnaeus, 1775, National Museum photo. 16S rRNA sequence Variable and conserved regions. Appl. Environ. Microbiol. (2006). 72(1): 733-744. Phylogenetic tree construction Tree of life based on 16-18S rRNA sequences  Amoeba Algae (eukaryote) (eukaryotes) Fungi (eukaryotes) Bacteria, Archaea (prokaryotes) Viruses Bacteria Mostly unicellular (with some notable exceptions, e.g. the fruiting bacteria and biofilms). Widely distributed. Cell wall of peptidoglycan. Two types of cells: – Gram negative – Gram positive Typical bacterial cell Typical eukaryote (plant) cell  Bacterial cell wall Credit: Gram cell wall: JulianOnions; Gram-positive: JA Jernigan et al./Centers for Disease Control and Prevention; Gram-negative: William A. Clark/Centers for Disease and Control; Source: Gram cellwall: http://commons.wikimedia.org/wiki/File:Gram-Cell-Wall.jpg; Gram-positive: http://www.cdc.gov/ncidod/EID/vol7no6/jerniganG2.htm; Gram-negative: 16S phylogeny of bacteria Brzuszkiewicz, Elzbieta et al. (2006) Proc. Natl. Acad. Sci. USA 103: 12879-12884 Copyright ©2006 by the National Academy of Sciences Archaea Separated from bacteria based on 16S rRNA gene sequence (Woese 1977). Lack peptidoglycan in the cell wall. Have different types of lipids in membrane (ether linkage). Mostly studied for life in extreme environments e.g. deep sea vents. Archaea: extreme environments Volcanic pool Hydrothermal vent Antarctic lake Archaea Crenarchaetoa – Thermophilic & hyperthermophilic. – Cool marine planktonic waters. Euryarchaeota – Methanogens – use H2 to reduce CO2 to CH4 – Halophiles – live in very high salt environments – Thermoacidophiles – have an optimum growth temperature between 60 – 80C; live at low pH. Protista (eukaryotes) – Unicellular eukaryotes that inhabit water and soil and feed on bacteria and small particles. – Reproduce sexually and asexually. – They absorb nutrients through their outer membranes or ‘wrap themselves around’ their prey to ingest. – Classification system is based primarily on motility and morphology. A sampling of protists, composed of images from Wikimedia Commons. Clockwise from top left: red algae (Chondrus crispus); brown algae (Giant Kelp); ciliate (Frontonia); golden algae (Dinobryon); Foraminifera (Radiolaria); parasitic flagellate (Giardia muris); pathogenic amoeba (Acanthamoeba); amoebozoan slime mold (Fuligo septica) CC BY-SA 4.0 https://commons.wikimedia.org/wiki/File:Protist_collage_2.jpg#/media/File:Protist_collage_2.jpg Viruses (more detail in coming lectures) Obligate intracellular parasites – cannot replicate by themselves. Have no machinery for making proteins, etc. Have limited host range determined by a viruses requirement for attachment to host cells (receptors). Belong to no kingdom. ds DNA, ss DNA, ds RNA, ss RNA – usually organised as single linear or circular molecule of nucleic acid. Viral structure Bacteriophage HIV Nucleic acid (DNA or RNA) Capsid – protein subunits – protect nucleic acids Receptors – host specificity Virus life cycles Lytic cycle Lysogenic cycle 1. Attachment 1. Virus attaches and injects DNA – 2. Penetration incorporation into host 3. Biosynthesis = PROPHAGE 4. Maturation 2. Prophage DNA passed on to daughter cells 5. Release 3. DNA can excise and enter lytic cycle Importance of mutants and mutation Mutations are caused by: Errors occurring during replication. Errors occurring during DNA repair – damage cause by: – UV – Chemicals (e.g. H2O2) – Other stresses (e.g. heat) DNA recombining after gene transfer from an external source.  Darwinian principle: Population Mutation Variant Selection New Population Mutation enable evolution! Mutants are always present within populations. Challenged with a new environmental factor (e.g. change in temperature) or opportunity (e.g. new source of nutrients), the fittest will survive and prosper. Evolution, fitness, survival – it’s a numbers game World’s population Feb. 2010: ~ 6.8 x 109 World’s population 2050: ~ 9 x 109 Number of people who have ever been born: ~ 1 x 1011 (in 2002) Number of microorganisms in 1 ml of clear seawater: ~ 105 – 106 Number of bacteria in 1 ml of a thick culture in your laboratory experiments: ~ 109 Number of bacteria and archaea in the World’s oceans: ~ 1030 Genetic selection: resistance 1 x 109 cells ml-1 0.00001% or 1/10 000 000 ampicillinr cells How many ampicillinr cells in 1.0 ml? How hard will it be to isolate an ampicillinr colony? Ampicillin containing plate Ampr colonies (1 x 109) x (1 x 10-7) = 1 x 102 in 1.0 ml Zone of inhibition Antibiotic disk Resistance mutants 28