Classification of Organisms

• Taxonomy - The Science that studies organisms to arrange them into groups
  • Taxa

Three separate but interrelated areas

Identification

• • • process of characterizing in order to group

Classification

• • • Arranging organisms into similar or related groups

Nomenclature

• • • system of assigning names

Previous classification schemes

• Whittaker (1960's) devised the 5 Kingdom Classification
  • plantae, fungi, animalia, Protista, and monera
  • The first four kingdoms are eukaryotes and the 5th is a prokaryote
• classification is often based on appearance and physiology

Current Classification Scheme

• Carl Woese with Kandler and Wheeler (1970s)
• Based on evolutionary relatedness (phylogeny) as determined by RNA

Domains

• • Eucarya
  • Bacteria (Eubacteria) > Prokaryotes
  • Archaea > Prokaryotes

Three domain system

Bacteria

• • Prokaryotic cell structure, no membrane-bound organelles
  • Ribosomal RNA nucleotide sequences that are unique to the group
  • Unicellular
  • Contains peptidoglycan

Archaea

• • Prokaryotic cell structure, no membrane-bound organelles
  • Ribosomal RNA nucleotide sequences that are unique to the group
  • Unicellular
  • No peptidoglycan

Eukarya

• • Eukaryotic cell structure, including a nucleus and other membrane-bound organelles
  • Ribosomal RNA nucleotide sequences that are unique to the group
  • Unicellular or Multicellular
  • No peptidoglycan

Hierarchical Scheme of Classification

Domain

• • relatively new taxonomy category that reflects the characteristics of the cells that make up the organism

Kingdom

Phylum

• • used in plant classification

Class

Order

• • In prokaryotic nomenclature, the name of the order ends with the suffix -ales

Family

• • In prokaryotic nomenclature, the name of the order ends with the suffix -acene

Genus

Species

• • A group of closely related isolates or strains
  • species can be subdivided into strains
  • not all members are identical

Determining Relatedness

How do we determine phylogeny for microorganisms?

• • more difficult for microorganisms
  • How to determine species with something that doesn't Sexually reproduce?
  • very few differences in Size and Shape
  • Traditionally used phenotypic characteristics but new advancements have allowed us to determine actual phylogeny
  • Informal phenotypic groupings are still a convenient way to categorize organisms and are based on a number of different categories.
    • Both phenotypic and genotypic

Using Phenotype

Microscopic Morphology

• • the first step in identifying a microorganism is to determine its Size, shape, and staining characteristics
  • Size and shape can put the organism into a broad category
  • Stains like gram stain and special Stains

Culture Characteristics

• • How does it grow, color, appearance, smell, growth on differential and selective media

Metabolic Capabilities

• • Biochemical tests, does it ferment, what does the organism react with

Serological Characteristics

• • serologial testing uses antibodies to detect specific proteins and polysaccharides
  • Different bacteria have different characteristics

Proton Profile

• • MALDI-TOF MS ( Matrix-assisted laser desorption ionization on time of flight mass Spectrom)
  • The type of mass spectrometry that determines the chemical composition of a Sample by measuring the masses of the various components
  • very fast

Using Genotype

Detecting Specific Nucleotide sequences

• • methods to detect nucleotide sequences unique to a given species or related group
  • makes it possible to identify organisms that can't be cultured
  • can only detect a single option

Nucleic Acid Amplification Tests (NAATs)

• • collective term including PCR
  • can defect a small amount of microorganisms and identify markers

DNA Probes

• • A tagged piece of single-stranded piece of DNA that is complementary to a sequence of interest is used to identify segments of DNA in the unknown microorganisms
  • fluorescence in situ hybridization (FISH)

Sequencing Ribosomal RNA Genes

• • nucleotide Sequence of ribosomal RNA molecules (RNA) or the DNA that encodes them (rDNA)
    • can be used to identify microbes

Whole Genome Sequencing

• • sequencing the whole genome
  • used to study outbreaks
  • can predict antibiotic resistance

Strains

• a group of related isolates
• All Members of a species are not Identical
• Strains May vary in minor ways
• has to be decided when an organism is sufficiently different to group as a different species

Binomial Nomenclature (Carl Linnaeus)

• Each species is identified by 2 names
• Genus is the first name
  • the first letter capitalized
• Species is the second name
  • no capitalization
• must be Italicized

Bacteria

• Single-celled prokaryotes
• small
• no nucleus or other organelles
• specific shapes
• most have rigid walls, contain peptidoglycan
• multiply via binary fission (asexual)
• Many have appendages (flagella)
• No introns/splicing
• 70s ribosomes
• Domain Bacteria
  • most bacteria are harmless or beneficial

Beneficial Microbes

• • • Prevent diseases by competing with pathogens
    • Development of immune system response
    • Aide in digestion
    • Food- Cheese and yogurt
    • Decomposers
    • oxygen production
    • Nitrogen fixation (plants)
    • use as a model organism
    • Genetic engineering
    • Bioremediation - use of organisms to remove or neutralize pollutants from a contaminated site
    • Microbes interact with us in ways we are just beginning to understand-microbiomes
  • Pathogenic microbes
  • some bacteria cause harm, disease, and death
  • Tuberculosis, tenatus, bubonic plague, diphtheria, food poisoning, syphilis, and leprosy

Archaea

common features

• • Prokaryotic and Unicellular
  • Small
  • specific shapes
  • look like bacteria
  • no nucleous or organelles
  • binary fission
  • can have appendages
  • Introns sometimes
  • 70s ribosomes
  • rigid cell walls without peptilogycan
  • Grow in extreme environments
    • high salt and other chemieals
    • extreme temps

Eukarya

common features

• • multicellular or single celled organisms
  • Eukaryotic cell structure
  • contains organelles
  • Large
  • has a nuclear membrane (no loose DNA)
  • Engages in mRNA splicing (mRNA has introns)
  • no peptidoglycan

Includes

Algae

• • • diverse group of photosynthetic eukaryotes, single or muti-celled

Fungi

• • • diverse group including yeasts and molds, single or multicelled

Protozoans

• • • A diverse group of single aquatic or terrestrial organisms. complex and large

Mammals

Helminths

• • • Parasitic worms that live at the expense of the host
    • Round worms, tapeworms, and flukes
    • Cause of disease, Particularly in developing countries
    • Adult worms are Macroscopic
    • eggs and larvae are microscopic

Acellular

Viruses

• • nucleic acid surrounded by a protein coat
  • needs host machinery to replicate
  • All forms of life can be infected

Viroids

• • simpler than viruses
  • short RNA without a protective coat
  • can only reproduce in cells
  • cause plant disease
  • some scientists speculate they may cause disease in humans.

Prions

• • only consist of protein
  • Infectious proteins: misfolded versions of normal cellular proteins in the brain
  • Abnormal form can cause fatal neurodegenerative diseases in humans and animals