Lecture 10: Taxonomy of Bacteria & Archaea Flashcards
What are the two ways to classify bacteria?
- Overall similarity (phenetic)
- Evolutionary relationships (Phylogenetics)
How long ago was the first evidence of microbial life?
3.5 by ago. (Earth is 4.5byo)
What is the best evidence we have of early life?
Stromatolites
What are stromatolites?
Microbial mats, layers of filamentous prokaryotes, sediments, and extracellular matrix.
True or false? Early earth was anoxic and hot.
True
What are ancient stromatolites?
Anoxygenic phototrophic filamentous bacteria.
What are moderm stromatolites?
Oxygenic phototrophic cyanobacteria
True or false? The 18s ribosomal subunit is found in prokaryotes.
False. Eukaryotes
What is the surface origin hypothesis?
1st membrane enclosed self repilcating cells arose out of primondial soup rich in organic/inorganic compounds on earths surface
What is the problem with the surface origin hypothesis?
Earth’s surface was not hospitable. Dramatic temp fluctuations (day/night), meteor impacts, dust clouds, UV, storms
What is the subsurface origin hypothesis?
- life originated in hydrothermal vents on ocean floor
- more stable conditions
- steady and abundant supply of energy
True or false. Archaea are often extremophiles.
True
What role did hydrothermal vents play in the origin of life?
- Nutrients in hot hydrothermal H20 flow up through mound
- mineral pores form compartments=first cells=RNA
- Compartments allow for coupling of energetic rxns to molecular replication
- eventually lipid bilayers took place of mineral compartments
What is the RNA world theory?
- First self-replication system may have been RNA based
- RNA can bind small molecules (ATP)
- RNA has catalytic activity, may have catalyzed it’s own synthesis (can be copied like DNA)
How did the great oxidation event occur?
In Archaen eon-origin of cyanobacteria creates so much O2 that it created possibility for eukaryotic life
What is phylogenetic classification?
Evolutionary relationships.
-Mutations, gene duplication, gene loss, HGT
What is an adaptive mutation?
Improve fitness of organism, increases survival
what is an deleterious mutation?
Decrease fitness of organism, decreases survival
What did Carl Woese do?
- RNA sequencing if SSU RNA (16s in prokaryotes, 18s in eukaryotes)
- Established presence of 3 domains of life
- Provided unified phylogenetic framework for bacteria
- Came up with RNA world theory
- Comparative rRNA sequencing
What is comparative rRNA sequencing?
- Amplification of gene encoding SSU rRNA
- Sequencing of amplified gene
- Analysis of sequence in reference to other sequences
What is SSU rRNA?
Conserved and highly variable region, accumulates neutral mutations over time (genetic drift)
-Few ssu rRNA differences=closely related
How do you sequence rRNA?
- Sequence 16s rRNA (Isolate DNA, amplify by PCR)
- Align sequences (take into acct. insertion/deletion)
- Look for similarities, count up base changes
- 5.
True or false. Eukaryotic cells are chimeric.
True (formed from various parts)
How do you sequence rRNA?
- Sequence 16s rRNA (Isolate DNA, amplify by PCR)
- Align sequences (take into acct. insertion/deletion)
- Look for similarities, count up base changes
- Construct phylogenetic tree
How do you construct a phylogenetic tree?
(Branch length represents # of changes) (Nodes = common ancestor) 1. Align sequences 2. calculate difference graph from # of sequence differences 3. Construct forked tree
What is the hypothesis of the endosybiotic origin of eukaryotes?
Mitochondria and chloroplasts arose from symbiotic association of prokaryotes within another type of cell=primitive eukaryote
What are the two different hypotheses on how eukaryotes gained mitochondria and chloroplasts?
- Eukaryotes began as a nucleus bearing lineage that later acquired mitochondria & chloroplasts by endosymbiosis
- Eukaryotic cells arose from intracellular association between a H2 producing bacterium (symbiot) and that later became a mitochondria. Host later developed nucleus
What are filamentous actinobacteria? (Streptomyces)
- Filaments elongate from their ends and form branching hyphae
- Cytoplasm separated by cross walls
- produce desiccation resistant spores @ tip of sporophore when nutrients depleted
What are predatory bacteria? (Bdellovibrio)
- Infect other bacterial cells, acquire nutrients from host
- doesn’t grow on agar, gram + bact. not affected
What are stalked bacteria? (Caulobacter)
- Found in aquatic environments
- chemoorganotroph
- undergoes unequal binary fission
- sedentary stalked mother cell and motile flagellated daughter cell (swarmer cell)
What are obligate intracellular bacteria? (Chlamydia)
- Parasites, grow only inside host cells
- start as elementary body (infectious)
- Host takes in elementary body thru phagocytosis
- inside Host=reticulate body, non infectious
- Reticulate body converts to elementary=lysis
What is the polyphasic approach to taxonomy?
Phylogenetic analysis+phenotypic analysis+genotypic analysis
What is multilocus sequence typing?
- Type of phylogenetic analysis
- looks at housekeeping genes
- sequence and align different housekeeping genes from same species
- sufficient resolving power to distinguish between closely related strains
- identify new strains this way
How do you identify an unknown organism?
Look at: Morphology Biochemical properties 16s gene MLST
What is a dichotomous key?
Graph that you can follow to see what characteristics an organism has:
- Gram stain
- glucose fermentation/morphology
- Motile @ 37C?
- Urea hydrolyzed?
- Indole produced/citrate utilized
What are 2 differential and selective methods to identify organisms?
Glucose fermentation and API strips
How can glucose fermentation be used to identify an organism?
If organism can ferment glucose, media will change from red to yellow
How can API strips be used to identify an organism?
Analytical profile index, fast identification through a series of small reaction tubes with indicators.
What is serotyping?
Based on binding of specific antibody to surface structure
Antibodies recognize and bind to molc on surface of microorganism/secreted proteins
What is a serotype?
Separate groups within a species that share similar characteristics (ie Same # of antigens on surface)
- LPS: O serotypes
- Capsule: K serotypes
- Flagella: H serotypes
