🦠 Taxonomy – Bacteria (Expanded Revision)
Taxonomy: the science of naming, describing, and classifying organisms into groups based on
shared characteristics. It has 3 branches:
1. Nomenclature- the system of naming organisms (ex: binomial names like Escherichia
coli).
2. Classification- grouping organisms based on relationships or similarity.
a. Phenetic (overall similarity)- based on observable traits, regardless of
evolutionary relationships.
b. Phytogenic (evolutionary relationships)- based on shared ancestry and genetic
data. Uses fossil records, RNA sequencing, MLST.
3. Identification- determining the identity of an organism based on known groups.
🧫 Fossil Record & Early Life
Fossil record is poor for bacteria:
o Bacteria do not fossilize well due to their small, soft bodies.
o Most evidence is indirect or based on ancient sediment structures.
Stromatolites:
o Rock-like structures formed by layers of microbial mats (dense communities of bacteria).
o Often made by phototrophs:
Phototrophs: Organisms that capture light energy to produce ATP.
These were likely among the earliest life forms on Earth.
🌋 Subsurface Hypothesis of Life's Origin life began deep in the ocean within hydrothermal vents
(subsurface environments in hydrothermal mounds), and life evolved step-by-step:
1. Hydrothermal mounds:
o Mineral-rich, warm environments under the sea with abundant chemical energy sources.
o Ideal for early chemical reactions that may have led to life.
2. Compartmentalization:
o Early life may have started in small, enclosed spaces (e.g., lipid bubbles) that separated internal
reactions from the external environment—this is a key feature of cells.
3. RNA World Hypothesis:
o Suggests that RNA came first, before DNA or proteins.
o RNA could both:
Store genetic information (like DNA),
Catalyze chemical reactions (like enzymes).
4. Proteins & DNA take over:
o Proteins: Became the main biological catalysts (enzymes).
o DNA: Became the primary molecule for long-term genetic storage due to its stability.
5. Lipid Membranes:
o Formation of phospholipid bilayers allowed for the creation of cells with controlled
environments.
6. HGT (Horizontal Gene Transfer):
o The movement of genes between organisms not by inheritance, but directly (e.g., through
plasmids, viruses).
, o Very common in early microbial evolution and still happens in bacteria today.
7. LUCA (Last Universal Common Ancestor):
o The most recent common ancestor of all living organisms.
o Thought to be a simple, single-celled organism.
o Developed into everything on the planet
🧬 Phylogenetic Analysis
Phylogenetics:
o The study of evolutionary relationships among organisms.
o Based on genetic data rather than appearance.
16S rRNA gene:
o A highly conserved gene present in all bacteria that codes for part of the ribosome.
o Its slow mutation rate makes it ideal for identifying and classifying bacteria at the genus or
species level.
MLST (Multilocus Sequence Typing): more accurate than 16S alone for resolving closely related strains
o Compares multiple housekeeping genes (genes essential for basic cell function and conserved
across strains).
o Used to:
Classify bacterial species and strains,
Track outbreaks of pathogens.
🧪 Classification of Strains
(A strain is a genetic variant or subtype of a species)
Methods used:
MLST: See above.
Phenotypic analysis:
o Observation of observable characteristics, such as:
Colony shape, colour, size
Metabolism (e.g., lactose fermentation)
Temperature/pH tolerance
Specific gene presence:
o PCR or other molecular tools used to check if a strain has a particular gene, e.g., a toxin or
resistance gene.
Serotyping: Identifies bacterial strains based on surface antigens:
O antigen (part of lipopolysaccharides in Gram-negative bacteria)
H antigen (flagellar protein)
🔍 Identification Methods: matching an unknown organism to known data using:
16S rRNA sequencing: for bacteria/eukarya
o Identifies unknown bacteria by comparing 16S rRNA gene sequences to databases.
MLST:
o Used for precise tracking and comparison of bacterial isolates.
Dichotomous key: you KNOW what you’re looking for helps narrow down possibilities
, o A step-by-step tool that guides you through binary choices based on features (e.g., Gram stain
+ shape + metabolism).
Serotyping:
o Distinguishes between strains of bacteria using antibody reactions to specific surface antigens.
Universal Phylogenetic Tree
🧬 WhatA universal
is it?
phylogenetic tree depicts the evolutionary relationships among all known forms of life,
based on molecular sequencing data, primarily:
o 16S rRNA (Bacteria & Archaea)
o 18S rRNA (Eukaryotes)
Introduced by Carl Woese, who:
o Discovered Archaea as a separate domain using SSU rRNA sequencing
🔁 o Replaced the 5-kingdom model with the three-domain system.
How it’s constructed:
Based on slowly evolving genes (like rRNA), allowing us to see deep evolutionary branches.
Molecular phylogeny is more accurate than phenetic (appearance-based) classification.
🔴 Common Ancestor
LUCA = Last Universal Common Ancestor
The hypothetical ancestor of all modern cells.
Believed to have had:
o Genetic material (likely RNA and/or DNA),
o Lipid membrane
o Basic metabolic pathways (glycolysis, ATP synthesis)
Chemoautotrophic lifestyle is believed to have been ancestral.
🟩 Domain: Bacteria
Prokaryotic (no nucleus, no membrane-bound organelles).
Reproduce asexually (binary fission), possess peptidoglycan in cell walls.
Often studied using phenetic traits and genotypic analysis (e.g., MLST, 16S rRNA).
Key Groups on the Tree:
Cyanobacteria: Oxygenic phototrophs; gave rise to chloroplasts (via endosymbiosis in algae and
plants).
Chloroflexus: Green non-sulfur bacteria, photoheterotrophs.
Purple bacteria: Early phototrophs; anoxygenic.
Flavobacteria: Gram-negative rods, often environmental.
Thermotogales & Aquifex: Hyperthermophiles; among the most ancient bacterial lineages.
Chloroplast lineage: A branch of cyanobacteria that was engulfed by a eukaryotic ancestor → primary
endosymbiosis.
🟪 Domain: Archaea
, Also prokaryotic, but biochemically and genetically distinct from bacteria:
o Unique ether-linked membrane lipids,
o No peptidoglycan,
o Often extremophiles.
Groups on the Tree:
Methanococcus / Methanothermus: Methanogens, produce methane (CH₄) from H₂ and CO₂.
Halophiles: Require high salt concentrations (e.g., Halobacterium).
Thermococcus / Pyrodictium / Thermoproteus: Hyperthermophiles, sulfur-reducing, found in hot
springs or hydrothermal vents.
🟦 Domain: Eukarya
Eukaryotes = cells with a nucleus, organelles, and linear chromosomes.
Originated from an Archaea-like ancestor that engulfed a bacterium → formed the mitochondrion
(endosymbiosis).
o Later, some eukaryotes also engulfed cyanobacteria → formed chloroplasts.
Groups on the Tree:
Multicellular lineages: Animals, Fungi, Plants.
Unicellular lineages:
o Diatoms, Ciliates, Slime molds,
o Flagellates, Diplomonads, Trichomonads,
o Microsporidia: Intracellular parasitic fungi.
Taxonomy – Eukaryotes
🔬 Phylogeny (evolutionary relationships)
Determined using MLST (Multilocus Sequence Typing) to make accurate evolutionary trees:
o Compares DNA sequences of several conserved genes.
o Helps track species-level and strain-level evolution.
🧪 Hydrogenosome (specialized organelle found in some anaerobic eukarya)
A membrane-bound organelle in some anaerobic protists (e.g., Trichomonas).
Function:
o Oxygen-free ATP production
o Converts pyruvate → H₂, CO₂, and acetate.
o Does not require oxygen (found in strictly fermentative organisms).
Thought to be evolutionarily related to mitochondria.
🧬 Mitosome
A degenerate (non-functional) mitochondrion found in organisms like Giardia.
No energy production, but:
o Helps in the maturation of iron-sulfur clusters (important for protein function).
Taxonomy: the science of naming, describing, and classifying organisms into groups based on
shared characteristics. It has 3 branches:
1. Nomenclature- the system of naming organisms (ex: binomial names like Escherichia
coli).
2. Classification- grouping organisms based on relationships or similarity.
a. Phenetic (overall similarity)- based on observable traits, regardless of
evolutionary relationships.
b. Phytogenic (evolutionary relationships)- based on shared ancestry and genetic
data. Uses fossil records, RNA sequencing, MLST.
3. Identification- determining the identity of an organism based on known groups.
🧫 Fossil Record & Early Life
Fossil record is poor for bacteria:
o Bacteria do not fossilize well due to their small, soft bodies.
o Most evidence is indirect or based on ancient sediment structures.
Stromatolites:
o Rock-like structures formed by layers of microbial mats (dense communities of bacteria).
o Often made by phototrophs:
Phototrophs: Organisms that capture light energy to produce ATP.
These were likely among the earliest life forms on Earth.
🌋 Subsurface Hypothesis of Life's Origin life began deep in the ocean within hydrothermal vents
(subsurface environments in hydrothermal mounds), and life evolved step-by-step:
1. Hydrothermal mounds:
o Mineral-rich, warm environments under the sea with abundant chemical energy sources.
o Ideal for early chemical reactions that may have led to life.
2. Compartmentalization:
o Early life may have started in small, enclosed spaces (e.g., lipid bubbles) that separated internal
reactions from the external environment—this is a key feature of cells.
3. RNA World Hypothesis:
o Suggests that RNA came first, before DNA or proteins.
o RNA could both:
Store genetic information (like DNA),
Catalyze chemical reactions (like enzymes).
4. Proteins & DNA take over:
o Proteins: Became the main biological catalysts (enzymes).
o DNA: Became the primary molecule for long-term genetic storage due to its stability.
5. Lipid Membranes:
o Formation of phospholipid bilayers allowed for the creation of cells with controlled
environments.
6. HGT (Horizontal Gene Transfer):
o The movement of genes between organisms not by inheritance, but directly (e.g., through
plasmids, viruses).
, o Very common in early microbial evolution and still happens in bacteria today.
7. LUCA (Last Universal Common Ancestor):
o The most recent common ancestor of all living organisms.
o Thought to be a simple, single-celled organism.
o Developed into everything on the planet
🧬 Phylogenetic Analysis
Phylogenetics:
o The study of evolutionary relationships among organisms.
o Based on genetic data rather than appearance.
16S rRNA gene:
o A highly conserved gene present in all bacteria that codes for part of the ribosome.
o Its slow mutation rate makes it ideal for identifying and classifying bacteria at the genus or
species level.
MLST (Multilocus Sequence Typing): more accurate than 16S alone for resolving closely related strains
o Compares multiple housekeeping genes (genes essential for basic cell function and conserved
across strains).
o Used to:
Classify bacterial species and strains,
Track outbreaks of pathogens.
🧪 Classification of Strains
(A strain is a genetic variant or subtype of a species)
Methods used:
MLST: See above.
Phenotypic analysis:
o Observation of observable characteristics, such as:
Colony shape, colour, size
Metabolism (e.g., lactose fermentation)
Temperature/pH tolerance
Specific gene presence:
o PCR or other molecular tools used to check if a strain has a particular gene, e.g., a toxin or
resistance gene.
Serotyping: Identifies bacterial strains based on surface antigens:
O antigen (part of lipopolysaccharides in Gram-negative bacteria)
H antigen (flagellar protein)
🔍 Identification Methods: matching an unknown organism to known data using:
16S rRNA sequencing: for bacteria/eukarya
o Identifies unknown bacteria by comparing 16S rRNA gene sequences to databases.
MLST:
o Used for precise tracking and comparison of bacterial isolates.
Dichotomous key: you KNOW what you’re looking for helps narrow down possibilities
, o A step-by-step tool that guides you through binary choices based on features (e.g., Gram stain
+ shape + metabolism).
Serotyping:
o Distinguishes between strains of bacteria using antibody reactions to specific surface antigens.
Universal Phylogenetic Tree
🧬 WhatA universal
is it?
phylogenetic tree depicts the evolutionary relationships among all known forms of life,
based on molecular sequencing data, primarily:
o 16S rRNA (Bacteria & Archaea)
o 18S rRNA (Eukaryotes)
Introduced by Carl Woese, who:
o Discovered Archaea as a separate domain using SSU rRNA sequencing
🔁 o Replaced the 5-kingdom model with the three-domain system.
How it’s constructed:
Based on slowly evolving genes (like rRNA), allowing us to see deep evolutionary branches.
Molecular phylogeny is more accurate than phenetic (appearance-based) classification.
🔴 Common Ancestor
LUCA = Last Universal Common Ancestor
The hypothetical ancestor of all modern cells.
Believed to have had:
o Genetic material (likely RNA and/or DNA),
o Lipid membrane
o Basic metabolic pathways (glycolysis, ATP synthesis)
Chemoautotrophic lifestyle is believed to have been ancestral.
🟩 Domain: Bacteria
Prokaryotic (no nucleus, no membrane-bound organelles).
Reproduce asexually (binary fission), possess peptidoglycan in cell walls.
Often studied using phenetic traits and genotypic analysis (e.g., MLST, 16S rRNA).
Key Groups on the Tree:
Cyanobacteria: Oxygenic phototrophs; gave rise to chloroplasts (via endosymbiosis in algae and
plants).
Chloroflexus: Green non-sulfur bacteria, photoheterotrophs.
Purple bacteria: Early phototrophs; anoxygenic.
Flavobacteria: Gram-negative rods, often environmental.
Thermotogales & Aquifex: Hyperthermophiles; among the most ancient bacterial lineages.
Chloroplast lineage: A branch of cyanobacteria that was engulfed by a eukaryotic ancestor → primary
endosymbiosis.
🟪 Domain: Archaea
, Also prokaryotic, but biochemically and genetically distinct from bacteria:
o Unique ether-linked membrane lipids,
o No peptidoglycan,
o Often extremophiles.
Groups on the Tree:
Methanococcus / Methanothermus: Methanogens, produce methane (CH₄) from H₂ and CO₂.
Halophiles: Require high salt concentrations (e.g., Halobacterium).
Thermococcus / Pyrodictium / Thermoproteus: Hyperthermophiles, sulfur-reducing, found in hot
springs or hydrothermal vents.
🟦 Domain: Eukarya
Eukaryotes = cells with a nucleus, organelles, and linear chromosomes.
Originated from an Archaea-like ancestor that engulfed a bacterium → formed the mitochondrion
(endosymbiosis).
o Later, some eukaryotes also engulfed cyanobacteria → formed chloroplasts.
Groups on the Tree:
Multicellular lineages: Animals, Fungi, Plants.
Unicellular lineages:
o Diatoms, Ciliates, Slime molds,
o Flagellates, Diplomonads, Trichomonads,
o Microsporidia: Intracellular parasitic fungi.
Taxonomy – Eukaryotes
🔬 Phylogeny (evolutionary relationships)
Determined using MLST (Multilocus Sequence Typing) to make accurate evolutionary trees:
o Compares DNA sequences of several conserved genes.
o Helps track species-level and strain-level evolution.
🧪 Hydrogenosome (specialized organelle found in some anaerobic eukarya)
A membrane-bound organelle in some anaerobic protists (e.g., Trichomonas).
Function:
o Oxygen-free ATP production
o Converts pyruvate → H₂, CO₂, and acetate.
o Does not require oxygen (found in strictly fermentative organisms).
Thought to be evolutionarily related to mitochondria.
🧬 Mitosome
A degenerate (non-functional) mitochondrion found in organisms like Giardia.
No energy production, but:
o Helps in the maturation of iron-sulfur clusters (important for protein function).
