The Microbial World And The Tree Of Life Flashcards
Robert Hook, Micrographia
1660
Ruska, 1931
First TEM
von Ardenne, 1937
First SEM
Describe TEM
Beam of electrons is transmitted through a specimen to form an image
Describe SEM
Scans surface with a focussed beam of electrons
STM
- scanning tunnelling microscope
- imaging at the atomic level
- Binnig and Heinrich, 1981
ETEM
- environmental transmission microscope
- collects electron micrographs of wet and/or uncoated specimens in the specimen chamber
Why might a specimen be wet/uncoated
Gaseous environment
How can we see viruses?
Electron microscopy
How big are viruses?
0.05-0.1 micromètre
How can we see mycoplasma?
Electron microscopy
Some under light microscopy
How big are mycoplasma?
0.1-0.5 micromètres
How can we see bacteria
Light microscopy / electron microscopy
How big are bacteria
1-10 micromètres
How can we see yeasts
Light microscopy / electron microscopy
How big are yeasts
3-10 micromètres
How can we see eukaryotic cells
Light microscopy
Up to 50 micromètres with electron microscopy
How big are eukaryotic cells
> 50 micromètres
How can we see mycelia
With the naked eye/ light microscopy
How big are mycelia
Bigger than 100 micromètres
Describe viruses
- infectious, often pathogenic
- typically smaller than bacterium
- very diverse size, morphology and composition
- obligate cellular parasites
- diverse genetic material
What do viruses do?
Reprogrammé cellular machinery to replicate themselves
Describe the diverse genetic material of viruses
- dsDNA
- ssDNA
- ssRNA
- dsRNA
List the components of a prokaryotic cell
- Cell wall
- Capsule
- Cell membrane
- Cytoplasm
- Nucleoid
- Plasmid
- Flagellum
Describe the components of a eukaryotic cell
- Plasma cell membrane
- Cytoplasm
- Mitochondrion
- SER
- RER
- Vacuole
- Golgi
- Nucleus
- Nucleolus
- Ribosomes
- Microtubules
- Centrosomes
- Microfilaments
- Lysosomes
- Secretory vesicles
- Peroxisomes
- Chromatin
- Intermediate filament
Describe bacteria
- single-celled microorganisms, diverse in shape and size
- widely distributed in range of environments
- cell wall usually contains peptidoglycan
- cell membrane fatty acids bound to glycerol with ester bonds in lipid bilayers
- glucose oxidation in glycolysis and Krebs cycle
- many examples of photosynthesis
Components of peptidoglycan
- N-acetylmuramic acid
- D-amino acids
Give an example of photosynthetic bacteria
Cyanobacteria
Describe archaea
- single called microorganisms, diverse in shape and size
- characteristically found in extreme environments
- cell walls of pseudopeptidoglycan, polysaccharides, glycoproteins, or proteins
- membrane lipids of phytanyl groups hound to glycerol with ether bonds, in bilayers, monolayers, or mixture
- glucose oxidation in glycolysis and Krebs cycle not described
- oxygenic photosynthesis not described
Give examples of extreme environments where archaea might be found
- deep sea hydrothermal cents
- hot springs
- salt brine
Compare and contrast the reproduction of bacteria and archaea
Bacteria: binary fission, some produce spores
Archaea: binary fission; sporulation not described
Compare and contrast the chromosomes of bacteria and archaea
Bacteria: usually a single circular chromosomes; introns not described
Archaea: usually a single circular chromosome; introns may be present
Compare and contrast the flagella of bacteria and archaea
Bacteria: hollow, assembled by adding subunit a from a central pore to the tip
Archaea: archella synthesised by adding subunits at the base
Archella
Archael flagella
Compare and contrast the tRNA of bacteria and archaea
Bacteria: thymine present
Archaea: thymine absent
Compare and contrast the tmRNA of bacteria and archaea
Bacteria: tmRNA not described
Archaea: described
Compare and contrast the RNA Polymerase of bacteria and archaea
Bacteria: simple, four polypeptides
Archaea: complex, >8 polypeptides, may have multiple
Compare and contrast the pathogenicity of bacteria and archaea
Bacteria: many
Archaea: none described
Early bacterial classification
- Haeckel’s Monera (morphology)
- Colony morphology
- Staining (Gram)
What allowed the introduction of colony morphology classification
Microbiology culture
Describe Gram negative bacteria
- two membrane cell wall
- thin layer of peptidoglycan
Describe Gram positive bacteria
- single cell membrane
- thick peptidoglycan and teichoic acid layer layer
Give examples of eukaryotic microorganisms
- Archaeplastida
- Rhizaria
- Chromoalveolata
- Excavate
- Amoebozoa
- Opisthokonta
Describe Archaeplastida
Plants, red and green algae
Describe Rhizaria
Mostly heterotrophic unicellular organisms
Describe Chromoalveolata
- Stramenopiles, unicellular flagellates and diatoms
- Alveolata
Describe Alveolata
- widespread group of predators and parasites
- e.g. Paramecium
Describe Excavata
- mostly heterotrophs
- some pathogenic
- many anaerobic
- Giardia, Trypanosoma
Describe Amoebozoa
Many forms of amoeba including Dictyostelium; slime moulds
Describe Opisthokonta
Fungi, animalia
How large is an amoeba?
150-400micrometres
How big is Giardia?
~10micrometres
Describe fungi
- can be micro/macroorganisme
- eukaryotic
- typically haploid nuclei
- reproduce mainly with sexual and asexual spores
- rigid chitin our cell walls
- mostly filamentous growth form
- heterotrophic
What is the fungal filament called?
Hypha
What is the fossil evidence of early bacterial life?
- stromatolites in carbonate sediments
- Cyanobacteria
- 3.4-3.5bn years ago (Archaen)
- abundant in the Proterozoic (2.8-3GA)
Impacts of microorganisms on human society
- Health
- Agriculture
- Food
- Industry
Microorganisms in health
- Microbiome
- Morbidity and mortality
Microorganisms in agriculture
- Leguminous plants
- Nitrogen fixation
- Ruminant microbiota in cattle and sheep
- Disease
Microorganisms in food
- Spoilage
- Fermentation
Microorganisms in industry
- Antibiotics
- Enzymes
- Chemicals
- Harmful
Microbes on évolution
- Symbiosis
- Disease
Microbes interacting
- Rhizosphère
- Microbiome
Bacteria make up
- 70bn tonnes carbon
- 12.8% total biomass
Fungi make up
- 12bn tonnes carbon
- 2.2% total biomass
Archaea make up
- 8bn tonnes carbon
- 1.5% total biomass
Protists make up
- 4bn tonnes carbon
- 0.7% total biomass
Viruses make up
- 0.2bn tonnes carbon
- 0.04% total biomass
Evolution of classification before molecular biology
- System Naturae (Carl Linnaeus)
- Tree of Life (Ernst Haeckel)
- Two Empires (Édourd Chaton)
- Four Kingdoms (Herbert Copeland)
- Five Kingdoms (Robert Whittaker)
Describe the Systema Naturae
Cataloguing and naming, introduced the Latin binomial
Describe the Tree of Life
- based on morphological complexities, tissue system and nutrition
- ideas of descent
Describe the Two Empires
eukaryotes and prokaryotes: cells with and without a nucleus
Describe the Four Kingdoms
Distinguished on cellular properties
Describe the Five Kingdoms
Cellular and nutritional characteristics
Describe rRNA
- accessible and tractable nucleic acid
- structural component of the ribosome
- functionally essential
- highly conserved
- relatively short (~1.5Kbp)
- various amount organisms (though mostly at genus level)
Among bacterial 16S rRNAs, there are
- several universal conserved regions used to generate sequencing primers
- nine variable regions used as phylogenetic signatures
How is rRNA characterised?
Thin layer chromatography sequencing
What does the endosymbiotic theory suffer
Mitochondria and chloroplasts are descended from specialised bacteria that survived endocytosis and became incorporated into the host cell
Extreme environments are
Rich in microbial life, and can support complex communities
Microbes
Dominate the biosphere
Problems with microscopy
- microscope bias
- staining: we are looking at artefacts
Archaeal polymerases are
Much more like us
Which Gram is probably ancestral?
Negative
What is extreme depends upon
Your perspective - anthropocentrisme, animal-centric, eukaryote-centric