Microbial Evolution, Taxonomy & Diversity Flashcards
Taxonomy (3) vs. Phylogeny (2)
Taxonomy
-Artificial classification of organisms
-Solely based on visible similarities
-Still used to name organisms
*Phylogeny
-Natural classification of organisms
-Reflects the evolutionary relatedness between organisms
Early Classification Schemes of living organisms
- Traditional early schemes: -Plants (plant, algae)
-Animals (animals, protozoa) - Ernest Haeckel’s proposal
-Plants (plants)
-Animals (animals)
-Microorganism (Protist: protozoa, fungi, algae, bacteria)
(in his tree of life, common ancestors but no interactions between groups) - Edouard Chatton
-Eukaryotes (plants, animals, algae, fungi, protozoa)
-Prokaryotes (bateria) - Robert Whittaker
-Monera (bacteria)
-Protista (Protozoa and algae)
-Fungi (fungi)
-Plantae (plants)
-Animali (animals)
5.Carl Woese
-Bacteria (bacteria)
-Archaea (bacteria)
-Eukaryotes (plants, fungi, protozoa, animals, algae)
3 groups equally distant
they use molecular approach (16S ribosome RNA)
Create a Phylogeny tree
-Sequence of a ubiquitous gene
-Find which sequences share the highest level of homology and link closest neighbors
-Create phylogenetic tree, branching the organisms related to the similarity of their gene sequence (The length of the branches linking the different organisms are proportional to their evolutionary distance)
Mitochondria and chloroplasts resemble prokaryotes (6)
- Approximately the same size (1 μM)
- The only organelles containing DNA (an active genome)
- Mitochondrial and chloroplastic genomes are circular
- They contain 70S ribosomes (80S in eucaryotes)
- Double membrane resemble cytoplasmic and outer membranes of gram-negative bacteria, however they do not have the cell envelope
- They multiply and divide by binary fission
What is the endosymbiotic theory of evolution?
Who propose it?
A primitive prokaryotic cell engulfed an ancient procaryote to create the first eukaryotic cell.
Lynn Margulis
Benefit of endosymbiotic relationship
Prokaryotic cell: having a sheltered environment rich in nutrients
Eukaryotic cell: containing an organism that produced energy (ATP) by respiration (mitochondria) or by photosynthesis (chloroplast)
Ancestor of mitochondria and chloroplasts
Mitochondria are the descendants of an alpha proteobacterium (gram-negative, Rickettsia prowazekii)
Interestingly R. prowazekiiis an obligate intracellular parasite
Chloroplasts are the descendants of a cyanobacterium (Prochloron)
Evidence of endosymbiotic theory
-Eucaryotes constantly phagocytoze prokaryotic cells (most time totally digest)
-Need time to co-evolve and create a stable new organism
Aphids and related insects (200million years)
-The endosymbiont still has its gram-negative double membrane and cell envelope, phylogenetically closely related to E. coli
-Stable endosymbiotic event:
1. The endosymbiont can no longer grow outside its host
2. Aphids are also dependent of their endosymbiont, they die if the endosymbiont is killed (antibiotic）
Timeline of evolution
Not same time for mitochondria and chloroplast (2.5 billion years later)
earth: 4.5 b ago
Prok: 3.5 b ago
Euk:1.0 b ago
Plants: 0.7 b ago
Goals and uses of Bacterial taxonomy
-Classification (biological classification)
-Nomenclature (how to name organisms)
-Identification (visible characteristics)
Goals of classification：
-Stability
-Predictability
-Build larger and larger groups (hierarchical)
-Study one member, learn about the group
The hierarchical scheme of classification
Kingdom or Domain
Phylum or Division
Class
Order
Family
Genus
Species (Basic taxon)
Name of bacterial species
-Binary combination of words in Latin form
-Consist of a genus name and a single epithet
-Genus name has an initial capital letter
-Species epithet with initial lower case
-Species name always italicized when printed and underlined when written
-Contraction of the genus after the first use in scientific texts
Info in name
- Appearance (Staphylococcus aureus)
- Habitat (Campylobacter jejuni, Helicobacter pylori)
- Characteristic property (Lactococcus lactis)
- Scientist name (Escherichia coli)
Concept of species in bacteriology
Species are divided into strains.
Different strains can have big genetic differences.
as long as the gene sequence didn’t change, it is the same stain.
Some gene can be shot down lead to the behavior change but the gene sequence remain the same
strains can difference in:
-biochemical or physiological differences (Biovars)
-different morphology (Morphovars)
-different antigenic properties (Serovars)
Numerical taxonomy Sj
similarity coefficient (Jacquard)
Sj=(# similarities shared)/(# similarities compare)
Equal weight to all compared character
Sj used to create dendograms
Traditional charaters (big category)
Morphology
Biochemistry and Physiology
Serology
Phage typing
Morphology (3)
*Shape (round, elongated, single, chains, clusters)
*Flagella (presence, location, number)
*Gram-stain (gram-positive, gram-negative)
Biochemistry and Physiology (6)
*Aerobic or not
*Optimal temperature
*Optimal pH
*Salt concentration
*Carbon source (96 well plates)
*Fermentation properties (produce acids or gases)
Serology
Antibodies against specific bacteria (antisera)
Phage typing (2)
*What bacteriophages can infect
*Bacteriophages have host range (infect only a limited number of bacterial cells)
Genomic characteristics
-Indirect methods (for taxonomy)
*G + C content (% G + C)
1. Melting point (more GC, temp. higher)
2. Density (more GC, higher density)
*DNA hybridization
1. Total genome hybridization
2. Probe hybridization (target a specific gene)
-Direct methods
Sequencing genes (rRNA, protein coding), give phylogenetic relationship, real evolutionary links
Major differences between prokaryotes and eukaryotes
Eukaryotes are more complex (organelles and compartments)
DNA contained in a membrane-bound structure (nucleus)
Bacterial cells are surrounded by a cell wall of peptidoglycan
Eukaryotic cells are approximately 10 times larger
Shape and arrangement of cells
*Spherical or ellipsoidal cells
-Cocci (singular, coccus)
*Cylindrical or rodlike
-Bacilli (singular, bacillus)
*Helical or spiral cells-
Spirilla (singular, spirillum)
-Vibrio (comma-shaped)
*Others-Irregular: square, star, et
cocci
coccus
diplococcus
tetrad
Sarcinae
streptococcus
staphylococcus
Rod-like
bacillus
coccobacillus
diplobacillus
streptobacillus
Spiral
spirilla
vibrio(comma-shaped)
some examples:
S. aureus
S. agalactiae
B. megaterium
Actinomyces
R.rubrum
V.cholerae
M. pneumoniae
Spiroplasma
Hyphomicrobium
G.ferruginea
Haloquadratum walsbyi
staphylococcus
streptococci
diplobacillus
filamentous
spirulum
vibrio(swim using its flagellla)
long rod, stick to surface
spirulim
“Hypha”
same strategy
archaea (s layer keep structure)
Colony morphologies
form
elevation
margin
texture
appearance
pigmentation
optical property
Form
punctiform
circular
filamentous
irregular
Rhizoid
spindle
elevation
flat
raised
convex
pulvinate
umbonate
Margin
more for （）
（fungi）
entire
undulate
lobate
erose
filamentous
curled
texture
smooth/rough
appearance
shinny or dull
pigmentation
non pigmented/colored
optical property
opaque（不透明的）/transparent
Bacteria cell vs Human cell
prokaryotic cells are smaller in size but have a higher surface to volume ratio allowing them to grow much faster
bacteria 1 um
human 10 um
Epulopiscium fishelsoni
-Gram+ (1993)
-very convoluted plasma membrane, like microvilli (more surface area)
-“guest at a fish’s banquet” —Found in the gut of the brown surgeon fish
-Symbiotic relationship with the surgeon fish
-First identified as a protozoon because of its size
-Size: 80 μm x 600 μm
-Volume: 1,000,000 times larger than E. coli
Thiomargarita namibiensis
Gram- (1997)
-Name means “sulfur pearl of Namibia”
-Found in ocean sediments (coast of Namibia)
-Size: 100 μm to 750 μm, 100,000,000 times larger than E. coli
-Volume: 100 times larger than E. fishelsoni
-can be seen by naked eye
huge nutrient vacuoles of nitrate in the middle
push the cytoplasm to the outside
Thiomargarita magnifica
Gram-(2022)
-Found in mangroves (Guadeloupe)
-Size: 100 μm to 9000 μm (almost 1 cm)
-Volume: 12,000,000,000 times larger than E. coli
-Size of an eyelash
Valonia ventricosa
alga
1836
-sea grape or sailor’s eyeball
-tropical and subtropical regions of various oceans
-Size: diameter of 5 cm
-Bigger than a golf ball
-multinucleated (ployploid) and multi organelles, only one membrane
Nanochlorum eukaryotum
1 to 2 μm in diameter
-About 10 times smaller than a human cell (10 μm)
-In the size range of a typical bacterial cell
-One true eucaryote Nucleus
-One mitochondrion
-One chloroplast
no space for multiple
-divide their nucleus and organelle first, then split into 2
