What is microbio?
- Study of organisms too small to see with the naked eye
- Bacteria viruses, single celled eukaryotes
- Micro bio is defined by techniques
- Culture media for isolation and growth is a pure culture
- Biochemical to study cell components
- Molecular and genetic techniques
Why is it important?
- Microbes are the oldest form of life
- Largest mass of living material on earth
- Carry out major processes for biogeochemical cycles
- Can live in places unsuitable for other organisms
- Other life forms require microbes to survive
Structure and activities of microbial cells
- All cells have the following in common
- Cytoplasmic membrane: barrier that separates the inside of the cell from the
outside environment
- Cytoplasm: aqueous mixture of macromolecules, ions, and proteins
- Ribosomes: site of protein synthesis
- Genetic material
- All cells store their genetic material as DNA
- The info is divided into functional units called genes
- Genome: a cell’s full complement of genes
- Chromosome: a genetic element carrying genes essential to cellular function
- Plasmid: a piece of DNA that carries non-essential genes
- E.g genes for antibiotic resistance
,Structural categorization of microbes
1. Eukaryotes
- Membrane bound nucleus
- Membrane bound organelles
- Complex internal organization
- Division by mitosis and meiosis
Protists: unicellular or multicellular without differentiation into tissues
- Protozoa: animal-like microorganisms
- Algae: photosynthetic plant-like microorganisms
- Slime molds and water mold: filamentous
Fungi: unicellular (yeasts), filamentous (molds), or multi-cellular (mushrooms)
2. Prokaryotes
- No membrane bound nucleus or organelles
- Generally smaller (aprox 1 ųm diameter)
- Simple internal structure
- Divide by binary fission
- Most are unicellular
Bacteria (eubacteria)
- Genetically diverse
- Extremely diverse metabolic styles
- Includes both pathogens and non-pathogens
Archaea (archaebacteria)
- Genetically and biochemically distinct from bacteria
- Also have diverse metabolism
- Never pathogenic
- Most famous for living in extreme environments
3. Viruses
- Acellular infectious particles
- Extremely small
- Obligate intracellular parasites
- Lack independent metabolism
- No ribosomes
- No ribosomal RNA
- Cannot be classified with other microbes
,Evolution and diversity of microbial cells
- First anaerobic life appeared between 3.8 and 3.9 billion years ago
- Photosynthetic bacteria oxygenated the earth about 2 billion years ago
- Allowed the evolution of modern eukaryotic microorganisms
- First plants and animals appeared about 0.5 billion years ago
Classifying organisms based on evolutionary relationships
- Comparing small subunit (SSU) rRNA genes
- Prokaryotes- 70S ribosomes
- 16S SSU rRNA
- Eukaryotes- 80S ribosomes
- 18S SSU rRNA
- rRNA genes change slowly over time
- Examines genetic differences rather than morphological differences
, Basic steps involved in sequencing rRNA genes
Step 1: DNA is collected from a pure culture
Step 2: the SSU rRNA gene is amplified using the polymerase chain reaction (PCR)
- PCR: a technique used to synthesized many identical copies of a short sequence
of DNA
Step 3: the gene is sequenced
Step 4: sequenced is aligned with sequences from other organisms
- Number of differences is used to calculate evolutionary distance
Phylogenetic tree: a graphic representation of the distance between organisms
Molecular phylogeny and the tree of life
- Phylogenetic tree based on 16S or 18S ribosomal DNA sequences
- All organisms can be grouped into 3 distinct domains of life
- Bacteria
- Archaea
- Eukarya
- Microorganisms are far more genetically diverse than plants and animals
The species concept in microbiology
- The species is the fundamental unit of biological diversity
- Phylogenetic species concept
- A group of strains that share a certain diagnostic traits are genetically cohesive
and have a unique recent common ancestor
- In practice species of bacteria and archaea should have
- Most (but not all) characteristics in common
- Greater than 97% sequence similarity in the 16S rRNA gene
- High degree of genome similarity
- DNA-DNA hybridization
Classification and nomenclature
- Microbiologists use hierarchical classification
- Groups of organism are placed in successively larger groups
- In practice: species, genus and phylum are commonly used
- Study of organisms too small to see with the naked eye
- Bacteria viruses, single celled eukaryotes
- Micro bio is defined by techniques
- Culture media for isolation and growth is a pure culture
- Biochemical to study cell components
- Molecular and genetic techniques
Why is it important?
- Microbes are the oldest form of life
- Largest mass of living material on earth
- Carry out major processes for biogeochemical cycles
- Can live in places unsuitable for other organisms
- Other life forms require microbes to survive
Structure and activities of microbial cells
- All cells have the following in common
- Cytoplasmic membrane: barrier that separates the inside of the cell from the
outside environment
- Cytoplasm: aqueous mixture of macromolecules, ions, and proteins
- Ribosomes: site of protein synthesis
- Genetic material
- All cells store their genetic material as DNA
- The info is divided into functional units called genes
- Genome: a cell’s full complement of genes
- Chromosome: a genetic element carrying genes essential to cellular function
- Plasmid: a piece of DNA that carries non-essential genes
- E.g genes for antibiotic resistance
,Structural categorization of microbes
1. Eukaryotes
- Membrane bound nucleus
- Membrane bound organelles
- Complex internal organization
- Division by mitosis and meiosis
Protists: unicellular or multicellular without differentiation into tissues
- Protozoa: animal-like microorganisms
- Algae: photosynthetic plant-like microorganisms
- Slime molds and water mold: filamentous
Fungi: unicellular (yeasts), filamentous (molds), or multi-cellular (mushrooms)
2. Prokaryotes
- No membrane bound nucleus or organelles
- Generally smaller (aprox 1 ųm diameter)
- Simple internal structure
- Divide by binary fission
- Most are unicellular
Bacteria (eubacteria)
- Genetically diverse
- Extremely diverse metabolic styles
- Includes both pathogens and non-pathogens
Archaea (archaebacteria)
- Genetically and biochemically distinct from bacteria
- Also have diverse metabolism
- Never pathogenic
- Most famous for living in extreme environments
3. Viruses
- Acellular infectious particles
- Extremely small
- Obligate intracellular parasites
- Lack independent metabolism
- No ribosomes
- No ribosomal RNA
- Cannot be classified with other microbes
,Evolution and diversity of microbial cells
- First anaerobic life appeared between 3.8 and 3.9 billion years ago
- Photosynthetic bacteria oxygenated the earth about 2 billion years ago
- Allowed the evolution of modern eukaryotic microorganisms
- First plants and animals appeared about 0.5 billion years ago
Classifying organisms based on evolutionary relationships
- Comparing small subunit (SSU) rRNA genes
- Prokaryotes- 70S ribosomes
- 16S SSU rRNA
- Eukaryotes- 80S ribosomes
- 18S SSU rRNA
- rRNA genes change slowly over time
- Examines genetic differences rather than morphological differences
, Basic steps involved in sequencing rRNA genes
Step 1: DNA is collected from a pure culture
Step 2: the SSU rRNA gene is amplified using the polymerase chain reaction (PCR)
- PCR: a technique used to synthesized many identical copies of a short sequence
of DNA
Step 3: the gene is sequenced
Step 4: sequenced is aligned with sequences from other organisms
- Number of differences is used to calculate evolutionary distance
Phylogenetic tree: a graphic representation of the distance between organisms
Molecular phylogeny and the tree of life
- Phylogenetic tree based on 16S or 18S ribosomal DNA sequences
- All organisms can be grouped into 3 distinct domains of life
- Bacteria
- Archaea
- Eukarya
- Microorganisms are far more genetically diverse than plants and animals
The species concept in microbiology
- The species is the fundamental unit of biological diversity
- Phylogenetic species concept
- A group of strains that share a certain diagnostic traits are genetically cohesive
and have a unique recent common ancestor
- In practice species of bacteria and archaea should have
- Most (but not all) characteristics in common
- Greater than 97% sequence similarity in the 16S rRNA gene
- High degree of genome similarity
- DNA-DNA hybridization
Classification and nomenclature
- Microbiologists use hierarchical classification
- Groups of organism are placed in successively larger groups
- In practice: species, genus and phylum are commonly used
