CH. 10 | Classification of Microorganisms

10 - 1 Define taxonomy, taxon, and phylogeny.

Taxonomy

• Classification and naming of organisms based on their shared characteristics, evolutionary relationships, and biological traits

• Uses similarities of organisms to identify, describe, name, and classify them. It does not account for evolutionary history
  
  
  → E. coli, a bacterium found in your gut. At the broadest level, it belongs to the domain Bacteria, meaning it's a single-celled organism with no nucleus. Zooming in further, it belongs to the family Enterobacteriaceae, a group of gut-dwelling bacteria. Its genus is Escherichia, and its full species name is Escherichia coli — the "coli" referring to the colon, where it lives.
  
  

Taxon

• Subdivisions are used to clarify organisms

• Examples include domain, kingdom, phylum, genes, species, etc
  
  

Phylogeny

• The evolutionary history of organisms, and the hierarchy of taxa, reflects their evolutionary, or phylogenetic, relationships

• How closely related they are through evolutionary history and shared ancestors

10 - 4 Discuss the advantages of the 3-domain system.

Reflective of evolutionary history, rather than cell history

• Before this 3-domain system, organisms were divided into prokaryotes and eukaryotes. However, differences in rRNA analysis revealed that 3 distinct cell lineages/types emerged (Bacteria, Archaea, and Eukarya)

• Supports evidence based on the classification of organisms into 3 domains because of their differences in rRNA

• By having 3 separate domains, the system more accurately captures the evolutionary split, rather than oversimplifying it into 2 groups
  
  

Archaea are fundamentally different from Bacteria

• Although archaea and bacteria are both prokaryotes, having them together in the old system was misleading

• Archaea lack peptidoglycan in their cell walls, and live in extreme environments, etc

• The 3-domain system gave Archaea its own domain, which is beneficial overall
  
  

Supported by molecular and genetic evidence

• Prokaryotic cells — 70S Ribosomes

• Eukaryotic cells — 80S Ribosomes

• Eukaryotic organelles, such as mitochondria, have 70S ribosomes, which share more similarities with prokaryotes than eukaryotes themselves

• These differences support separating life into 3 distinct domains rather than 2
  
  

Supports the Endosymbiotic Theory

• Eukaryotic organelles, such as mitochondria and chloroplasts, share similar characteristics with those of prokaryotes

• Same circular DNA, 70S ribosomes, binary fission reproduction

• The 3-domain system reveals how the eukarya domain evolved from early prokaryotic ancestors through endosymbiosis

10 - 5 List the characteristics of the Bacteria, Archaea, and Eukarya domains.

Bacteria

• Prokaryotes

• DNA is circular (some have two circular; some have linear)

• 70S ribosomes

• Cell Wall: Peptidoglycan

• Reproduction: binary fission

• Ester linkages
  
  

Archaea

• Prokaryotes

• DNA is circular

• 70S ribosomes

• Lack of peptidoglycan as their cell wall but have psudeomuerin

• Live in extreme environments — three major groups: Methanogens (produce methane), Extreme halophiles (require high salt), and Hyperthermophiles (grow in extremely hot environments)

• Ether linkages
  
  

Eukarya

• Eukaryotes

• DNA is linear

• They have 80S ribosomes

• Reproduction: mitosis

• They include the kingdoms Fungi, Plantae, and Animalia, as well as Protists

• Their organelles, like mitochondria and chloroplasts, share similarities with prokaryotes, supporting the endosymbiotic theory

10 - 6 Explain why scientific names are used.

Scientific names are used to identify the specific organism being discussed. Hence, explaining why common names are not good to use and are misleading

Each organism is assigned 2 names, the genus, and the specific epithet (species) — both are underlined or italicized — the genus name is always capitalized — the specific epithet is always lowercase

• Binomial nomenclature

• Ensures taxonomic accuracy
  
  

Taxonomic Hierarchy

• Domain - the broadest category; all life falls into Bacteria, Archaea, or Eukarya

• Kingdom - groups organisms by very broad characteristics (e.g., Animalia, Plantae, Fungi)

• Phylum - groups organisms by general body plan or fundamental biological traits

• Class - narrows down the phylum into more specific shared characteristics

• Order - groups families that are related to each other

• Family - groups of closely related organisms with fairly specific shared characteristics

• Genus - very specific grouping; becomes the first part of the scientific name

• Species - the most specific level; the second part of the scientific name
  
  

E. COLI EXAMPLE

• Domain → Bacteria

• Kingdom → Bacteria

• Phylum → Pseudomonadota

• Class → Gammaproteobacteria

• Order → Enterobacterales

• Family → Enterobacteriaceae

• Genus → Escherichia

• Species → Escherichia coli

10 - 8 Differentiate culture, clone, and strain.

Culture

• Microbes grown in culture media
  
  

Clone

• The population of cells derived from a single parent cell
  
  

Strain

• Genetically different subgroup of cells within a clone

• They are species

• Often distinguished using numbers, letters, or names that follow the specific epithet

• Examples include K-12 (Strain of E. coli)

10 - 9 List the major characteristics used to differentiate the 3 kingdoms of multicellular Eukarya.

Kingdom Fungi

• Can be unicellular or multicellular, or both

• Includes unicellular yeasts, multicellular molds, and macroscopic species such as mushrooms

• Obtains nutrients by absorbing dissolved organic matter through its plasma membrane (Heterotrophic)

• Multicellular fungal cells are joined to form thin tubes called hyphae

• Develops and replicates from spores or from fragments of hyphae
  → Differentiate endospores v. fungal spores
  
  

Kingdom Plantae

• Includes mosses, ferns, conifers, and flowering plants

• All members are multicellular

• Obtains energy through photosynthesis
  
  

Kingdom Animalia

• Includes sponges, worms, insects, and animals with backbones

• All members are multicellular

• Obtains nutrients and energy by ingesting organic matter through a mouth (Heterotrophic)

• No cell walls
  
  

Differing Characteristics

• Fungi absorb dissolved organic matter

• Plants produce their own energy through photosynthesis

• Animals ingest organic matter through a mouth

10 - 10 Define protist.

Protist

• Eukaryote, but is neither part of the fungi, plantae, or animalia kingdom

• Catchall kingdom for a variety of organisms

• Made up of diverse groups with differing characteristics

• Unicellular
  → Examples include amoeba, plasmodium, paramecium

10 - 11 Differentiate eukaryotic, prokaryotic, and viral species.

Eukaryotic

• Closely related organisms that can interbreed
  
  

Prokaryotic

• Reproduction is asexual

• Population of cells with similar characteristics

• Example includes E. coli | K12 & E. coli 0157: H7) — both shares similar characteristics

• Similar characteristics include morphology, biochemical reactions, and DNA sequences
  
  

Viral

• Having similar characteristics

• Morphology

• DNA structure

• Similar ecological niche
  → Host
  → Ecological niche, meaning where the virus lives

10 - 13 Explain the purpose of Bergey’s Manual.

Bergey’s Manual is a reference for bacterial ID and classification

• It is the standard taxonomic reference on bacteria

• Provides identification based on criteria such as cell wall composition, morpohlogy, differential staining, oxygen requirements, and biochemical testing