Microorganism Classification: Taxonomy and Phylogeny

• Chapter 10 focuses on the classification of microorganisms

Student Learning Outcomes

• Define taxonomy, taxon, and phylogeny
• List characteristics of the Bacteria, Archaea, and Eukarya domains
• Differentiate among eukaryotic, prokaryotic, and viral species
• Explain scientific naming
• Differentiate between culture, clone, and strain
• Compare and contrast classification and identification
• Explain the purpose of Bergey’s Manual
• Describe how staining and biochemical tests are used to identify bacteria
• Explain how serological tests and phage typing identify an unknown bacterium
• Describe how a microbe can be classified by ribotyping, DNA fingerprinting, and PCR
• Describe how microorganisms can be identified by nucleic acid hybridization, DNA chips, and FISH
• Explain and apply a dichotomous key

Taxonomy and Phylogeny

• Taxonomy is the science of classifying organisms, providing universal names
• Taxon/Taxa are taxonomic categories
• Phylogeny (systematics) refers to the evolutionary history of a group of organisms
• Taxonomic hierarchy displays phylogenetic/evolutionary relationships
• In 1969, living organisms were divided into five kingdoms
• In 1978, two types of prokaryotic cells were found: Prokaryotic relationships determined by rRNA sequencing
• All Species Inventory spans 2001-2025

Three-Domain System

• All organisms evolved from cells that formed over three billion years ago
• DNA passed on from ancestors is described as conserved
• The Domain Eukarya includes the kingdoms Fungi, Plantae, and Animalia, also including the protists
• Living organisms are classified into three domains based on similarities in ribosomal RNA: Bacteria, Archaea, and Eukarya (Key Concept)
• The three domains are bacteria, archaea, and eukarya

Characteristics of the Domains

• Eubacteria are virtuosos, Archaea are "weirdoes," and Eukarya are predators and thieves
• Carl Woese discovered the three domains in 1978
• Cell type: Archaea and Bacteria are prokaryotic, while Eukarya are eukaryotic
• Cell Wall: Archaea varies in composition but doesn't contain peptidoglycan; Bacteria contains peptidoglycan; Eukarya varies and contains carbohydrates
• Membrane Lipids: Archaea has branched carbon chains attached to glycerol by ether linkage; Bacteria possesses straight carbon chains attached to glycerol by ester linkage; Eukarya features straight carbon chains attached to glycerol by ester linkage
• First Amino Acid in Protein Synthesis: Archaea and Eukarya use methionine; Bacteria utilizes formylmethionine

Endosymbiotic Theory: Origin of Eukaryotes

• In the endosymbiotic theory, ancestral cells' plasma membrane through infoldings gave rise to endomembrane components including a nucleus and endoplasmic reticulum
• In the first endosymbiotic event, the ancestral eukaryote consumed aerobic bacteria that evolved into mitochondria
• In the second endosymbiotic event, the early eukaryote consumed photosynthetic bacteria that evolved into chloroplasts

Scientific Nomenclature

• Common names for organisms can vary by language and geography
• Binomial Nomenclature consists of genus + specific epithet and is used worldwide e.g. Escherichia coli, Homo sapiens

Scientific Names Origin

• Klebsiella pneumoniae: Honors Edwin Klebs with the epithet referring to the disease
• Pfiesteria piscicida: Honors Lois Pfiester with the epithet, referring to the disease in fish
• Salmonella typhimurium: Honors Daniel Salmon with the epithet, referring to stupor in mice
• Streptococcus pyogenes: Chain of cells, form pus
• Penicillium chrysogenum: Tuftlike, produce yellow pigment
• Trypanosoma cruzi: Corkscrew-like, Honors Oswaldo Cruz

Classification: Species Definition

• Eukaryotic species: Closely related organisms that breed among themselves
• Prokaryotic species: Population of cells with similar characteristics
• Bergey's Manual of Systematic Bacteriology is a standard reference for bacterial classification
  • Culture: Grown in laboratory media
  • Clone: Population of cells derived from a single cell
  • Strain: Genetically different cells within a clone
• Viral species: Population of viruses with similar characteristics, occupying a particular ecological niche
• Viruses aren't placed in kingdom nor domain; they are not composed of cells and can't grow without a host cell

Phylogenetic Relationships of Prokaryotes

• Bacteria include gram-positive bacteria, cyanobacteria, chlamydias, spirochetes, proteobacteria, and green sulfur/nonsulfur bacteria
• Archaea includes methanogens, extreme halophiles, and hyperthermophiles

Domain Eukarya Characteristics

• Animalia: Multicellular; no cell walls; chemoheterotrophic
• Plantae: Multicellular; cellulose cell walls; usually photoautotrophic
• Fungi: Chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments
• Protista: Catchall kingdom for eukaryotic organisms not fitting other kingdoms, grouped into clades based on rRNA

Prokaryotes Nutritional Modes

• Prokaryotes exist in every nutritional class

Prokaryote Nutritional Classifications

• Photoautotroph: Light energy source and CO2 carbon source. e.g. Cyanobacteria
• Chemoautotroph: Inorganic chemical energy source and CO2 source. e.g. Sulfolobus
• Photoheterotroph: Light energy source and Organic compound source. e.g. Rhodobacter, Chloroflexus
• Chemoheterotroph: Organic compound energy and carbon source e.g. Clostridium

Classification and Identification

• Classification places organisms in related species groups and lists known organism characteristics
• Identification matches characteristics of an "unknown" organism to lists of known organisms

Identifying Bacteria

• A flow chart shows examples of tests to identify bacteria
• These include gram reaction, glucose fermentation, motility, citrate utilization, indole production, and urea hydrolysis

Bergey's Manual

• the Manual of Determinative Bacteriology provides identification schemes for bacteria and archaea based on morphology, differential staining, and biochemical tests
• the Manual of Systematic Bacteriology provides phylogenetic data on bacteria and archaea based on rRNA sequencing

Methods for Classifying and Identifying Bacteria

• Classification uses morphological characteristics, differential staining, DNA base composition, DNA fingerprinting, PCR, Nucleic Acid Hybridization and rRNA Sequencing
• Identification uses differential staining, morphological characteristics, biochemical testing, serology, phage typing, fatty acid profiles, flow cytometry, DNA fingerprinting, PCR, and Nucleic Acid Hybridization

Clinical Lab Identification

• Morphological characteristics are useful for identifying eukaryotes
• Differential staining like Gram staining and acid-fast staining is performed
• Biochemical tests determine the presence of bacterial enzymes

Serology

• Involves reactions with specific antibodies: Combine known antiserum with unknown bacterium, useful for determining strains, species, as well as relationships among organisms
• Examples: Slide agglutination, ELISA, and Western blot

Phage Typing

• Used for bacterial species and strains identification, by determining their susceptibility to various phages

Genetics classification methods

• DNA fingerprinting: Number and sizes of DNA fragments (fingerprints) produced by RE digests are used to determine genetic similarities
• Ribotyping: rRNA sequencing
• Polymerase Chain Reaction (PCR): It can amplify a small amount of microbial DNA in a sample. The presence or identification of an organism is indicated by amplified DNA

Nucleic Acid Hybridization

• Single strands of DNA or RNA from related organisms will hydrogen-bond to form a double-stranded molecule
• This bonding is called nucleic acid hybridization and some applications include: Southern blotting, Northern blotting, DNA chips, and FISH.

Key Characteristics of Prokaryotes

• Nucleoid: Region of cytoplasm where prokaryote's genome (DNA) is located, usually a singular, circular chromosome
• Plasmid: Small extra piece of chromosome/genetic material with 5-100 genes, not critical to everyday functions, but can provide genetic information such as antibiotic resistance & virulence factors.
• Cytoplasm: Also known as protoplast, is a gel-like matrix of water, enzymes, nutrients, wastes, and gases
• Cytoskeleton: Cellular scaffolding within the cytoplasm
• Ribosomes: Found within cytoplasm or attached to the plasma membrane, are made of protein & rRNA and composed of two subunits
• Plasma Membrane: Separates cells from their environment

Bacterial Classification and disease

• Classification of Bacteria is Based on Shape, Staining, Action, Oxygen requirements, pH, Temperature, Structure, and Osmotic Pressure
• Pathogenic (parasitic) Prokaryotes cause about half of all human diseases ( e.g. Mycobacterium tuberculosis)

Symbiotic Relationships

• Living in close relationship for a long time. In this relationship, one of the organisms benefits
• There are three types: -Mutualism (+/+); both organisms benefit (e.g., human intestinal bacteria), -Commensalism (+/0); one organism benefits, and the other isn't affected -Parasitism (+/-); one organism benefits, and the other is harmed through exotoxins, toxic proteins secreted by pathogenic bacteria.

Types of Genetic Transference

• Conjugation (cell-to-cell contact through pilus),
• Transformation (uptake and incorporation of genetic material),
• Transduction (bacteriophages infect cells and transfer genetic material).

Benefitial Processes

• Bioremediation: Use of organisms to remove pollutants from the environment used in Research, Technology and Society
• Convert milk to cheese / yogurt
• E coli Cloning
• Agrobacterium tumefaciens to make transgenic plants

Dichotomous Key

• Animation tutorial provided