exam 2 Flashcards
Name of Archaea before they were recognized as a separate domain
Archaeabacteria
Habitats where Archaea were first identified and studied
Hot springs of Yellowstone National Park
3 characteristics that distinguished Archaea from bacteria that were the basis for their recognition as a domain of life
- Archaeal lipids
- Archaeal cell walls
- Archaeal genome
Advantages that Dr. Carl Woese suggested that would come from having a 3 domain organization of the tree of life
- Provide a more natural system of classification
- Take out the assumption that plants and animals are more important evolutionarily
- Foster the understanding of diversity of ancient microbial lineages
Similarity between Bacterial and Archaeal chromosomes and plasmids
Both are circular
Similarity between Bacterial and Archaeal DNA
DNA not contained within a membrane
Similarity between Bacterial and Archaeal infrastructure
No organelles
How lipids in Archaea are different from lipids in Bacteria
Archaeal lipids use L-glycerol, not D-glycerol like Bacteria, and therefore have ether linkages, not ester linkages; More branched
Selective advantage Archaeal lipids provide them
Allows them to be more resistant to harsher conditions
Why the Archaeal cell wall is resistant to lysozyme that can degrade Bacterial cell walls
Archaeal cell wall is made of pseudopeptidoglycans with a different beta-linkage than the one found in peptidoglycan that lysozyme attacks
3 similarities between Archaea and Eukaryotes?
- Presence of introns
- RNA polymerase
- Presence of histone homologues
5 phyla within the domain Archaea
- Halobacterium
- Haloferax
- Archaeoglobus
- Methanococcus
- Pyrococcus
Metabolism of Archaea within “Thaumarchaeota” or “Wonder Archaea” that is important in environmental nutrient cycling
Ammonia-oxidizers, the first step of nitrification
Phylum within the domain Archaea that is the most closely related to the branch that evolved to become the domain Eukarya
Lokiarchaeota
Habitat where you would be likely to find members of the Crenarchaeota
Hot springs
Tetraether produced by Crenarchaeota members that helps them survive extremely high temperatures
Crenarchaeol
Example of a temperature and pH at which you might find a Crenarchaeota in a hot spring
70-100C, pH 5-9
Oxidized by Delsulforococcus
Organic molecules
Reduced by Desulforococcus
Elemental sulfur
End product of redox reaction by Desulforococcus
Hydrogen sulfide gas
Found in association with Ignicoccus islandicus in deep thermal vents
Nanarchaeon symbiont
Oxidized by Ignicoccus islandicus
H2
Reduced by Ignicoccus islandicus
Elemental sulfur
End product of redox reaction by Ignicoccus islandicus
Hydrogen sulfide gas
Pyrodictium species metabolism
Heterotrophs or lithotrophs
Pyrodictium species live in deep sea vent ecosystems within this protease-resistant structure where there are extreme temperature gradients
Hyperthermal biofilms
Produced by Pyrodictium species
Network of hollow cannulae
Hollow cannulae network of Pyrodictium spp. is used to connect what part of cells?
Periplasm
Sulfolobus solfataricus metabolism
Heterotroph and lithotroph
Similar to Eukaryotes, Sulfolobus solfataricus has 2 of these
Origins of replication
Technique used to identify psychrophilic Thaumarchaeota as being abundant in the deep ocean
Fluorescent In-Situ Hybridization (FISH)
3 examples of environments in which Thaumarchaeota have been discovered
- Deep sea depths off Hawaii
- Roots of tomato plants
- With sponges
Metabolism of Thaumarchaeota that helps them contribute to the N cycle
Lithotrophic/ammonia oxidizers
Thaumarchaeota fix this from the atmosphere
CO2
Environmental consequence of methane emissions
Greenhouse gas
Sources of methane emissions
- Enteric fermentation
- Rice cultivation
- Wastewater
What inhibits metabolism of methanogens?
Oxygen/aerobic environments
Phylum of the domain Archaea where you find methanogens
Euryarchaeota
Prefix for each genera of methanogenic Archaea
Methano-
Morphology of methanogens
Diverse morphology –spiral, cocci, and rods
2 components that can comprise the Archaeal cell wall
- No cell wall, only an S layer
2. Pseudopeptidoglycan
Substrates required for the metabolism of methanogens
CO2 (terminal electron acceptor), H2 (electron donor), and Na+
Unique component of methanogenic Archaea that transfer hydrogen and reduced carbon to each enzyme in the pathway
Cofactors
Gradient required for methanogens to import H2
Sodium (Na+)
2 microorganisms that are metabolically dependent on each other
Syntrophic consortium
Waste product produced by acetogens that is used as an electron donor by methanogens
H2
Habitats where you would find methanogens
- Anaerobic soils of wetlands
- Digestive tracts
- Landfills
Compound produced by combining water and methane under very low temperatures and high pressure
Methane hydrate
Potential benefit and concern associated with the formation of methane hydrate
There is a lot of energy locked up in the compound, but even if a small amount is released into Earth’s atmosphere, it would have serious effects
Term that means “salt loving”
Halophilic
Phylum of Archaea where you would find salt-loving species
Euryarchaeota
2 pigments made by salt-loving archaea
- Bacterioruberin
2. Bacteriorhodopsin
Function of bacterioruberin
Protects halophiles from light
Function of bacteriorhodopsin
Absorbs light of a certain wavelength to generate a proton gradient to power ATP synthesis
Strategy used by salt-loving Archaea that enables them to survive and grow at high salt concentrations
Maintain high intracellular KCl concentration, have DNA with a higher G-C content, and have proteins with more acidic amino acids
Unique Archaeal morphology discovered by Professor Walsby
Square cells
Internal structure observed by Professor Walsby
Gas vesicles
pH range observed for salt-loving Archaea
7-10
3 examples of habitats where you can find salt-loving Archaea
- Thalassic lakes
- Athalassic lakes
- Solar salterns
Relationship between sensory rhodopsins, bacteriorhodopsins, and halorhodopsins
Paralogs
Relationship between bacteriorhodopsins and proteorhodopsins
Orthologs
How were proteorhodopsins discovered?
Metagenomic study of DNA from SAR11 with an rRNA operon
Metabolism of Thermococcales
Heterotrophs that use sulfur as a terminal electron acceptor to reduce sulfur
Where you would find Pyrococcus furiosus from Thermococcales
Deep sea vent
Characteristic of Pyrococcus furiosus
Monopolar polytrichous archaella
Where Ferroplasma get their energy
Oxidizing ferrous iron
Extreme environment where Ferroplasma can grow
Low pH
Method used to assemble Ferroplasma genome from biofilm samples collected from Iron Mountain mine
Shotgun sequencing?
The 2 major phyla of Gram-positive bacteria
Phylum Firmicutes and Phylum Actinobacteria
G-C content of Firmicutes
Low
G-C content of Actinobacteria
High
In what bacterial superphylum would you find Firmicutes and Actinobacteria
Superphylum Terrabacteria
Characteristics of a Gram-positive bacterial membrane and cell wall
- Have thick cell walls that retain crystal violet stain
- Cell walls reinforced by teichoic acids
- No outer membrane, but have a cytoplasmic membrane
Environment where you are most likely to encounter a high abundance of Gram-positive bacteria
Soil and sediment environments
Best known genus of aerobic endospore formers
Bacillales
Best known genus of anaerobic endospore formers
Clostridiales
Environmental extremes that endospores are resistant to
Hostile physical and chemical conditions
Cascade of these molecules drives a developmental process responsible for endospore formation
Sigma factors
Induces the sigma factor cascade
Starvation
Model bacterial species for the study of endospore formation
Bacillus subtilis
Toxin involved in Botox
Botulinum
Species that produces the toxin used in Botox
Clostridium botulinum
Introduces the genes responsible for the production of Botulinum toxin
Phage
How phage carrying botulinum toxin has been incorporated into bacteria
Lysogenic conversion
How Epulopiscium fishelsioni produces its offspring
Live birth
Genus containing one of the most primitive photosystems
Heliobacterium
Very dangerous food borne pathogen that does not produce a spore but is highly motile and is invasive in people
Listeria monocytogenes
System used by Listeria monocytogenes that makes it highly motile
Actin propulsion system
Genus of bacteria used for producing sauerkraut
Lactobacillus
Facultative anaerobic bacterium that forms clusters of cells and can result in life-threatening skin and heart infections in people
Methicillin-resistant Staphylococcus aureus (MRSA)
Unique features of bacteria within the phylum Tenericutes
- Lack a cell wall
- Have sterols that make the membrane more rigid
- Obligate intracellular pathogens
2 other species that are genetically similar enough to Bacillus cereus to be considered the same species, but have unique phenotypes
Bacillus anthracis and Bacillus thuringiensis
Famous German scientist that determined the causative agent for the disease Anthrax
Robert Koch
Required by the bacterium responsible for Anthrax to be fully virulent
2 plasmids, pxO2 and pxO1
Encodes for an antiphagocytic capsule
pxO2
Encodes for 3 exotoxin components
pxO1
3 exotoxin components of pxO1
- Protective antigen
- Edema factor
- Lethal factor
Occupations that put humans at greater risk for being exposed to the bacterium that causes Anthrax
Exposure to livestock, wool and hides, and laboratory settings
The most deadly form of Anthrax
Inhalation
Why the use of antibiotics is not usually effective at preventing mortality from Anthrax
Production of spores and delayed germination after antibiotic suppression
Type of disease caused by Bacillus cereus
Foodborne illness
Toxin produced by emetic strains of B. cereus
Cereulide
Genetic element that carries the genes responsible for the toxin produced by emetic strains of B. cereus
Peptide produced by non-ribosomal peptide synthesis (NRPS)
Where Bt toxin binds in an insect or other host
Specific receptors in the gut
Bacterial species from which a Bt toxin is produced
B. thuringiensis
Also responsible for the Bt toxin to have insecticidal activity
Other gut bacteria sometimes required for Bt binding
How the Bt toxin has been used in modern agriculture
Used to create genetically modified plants like corn, soybeans, and cotton to protect them from insects
Environments or hosts in which you would look for B. cereus, B. anthracis, and B. thuringiensis
Silkworms or flour moths?
Environment that would be predicted to include diverse Actinobacteria species
Soil
What many Actinobacteria use as a source of energy
Decomposing organic matter (i.e. cellulose, chitin)
Unusual characteristics of Streptomyces species that make them highly complex with large genomes
- Produce many antibiotics
- Have telomeres
- Genome has a high G-C content
Streptomyces life cycle
- Spore
- Germinating spore
- Vegetative mycelium
- Aerial hyphae
- Spore chains
A compound produced in the stationary phase of life
Secondary metabolite
Example of a secondary metabolite
Antibiotics
Why some bacteria like Streptomyces devote considerable energy to produce secondary metabolites
They can help the organism compete for limited resources
Why members of Actinobacteria were confused with fungi in the past
Because of convergent evolution they resemble filamentous fungi and also produce a spore
Example of a symbiotic association between a eukaryotic host and a species of Actinobacteria
Leaf-cutter ants and Actinobacteria
Select pressures that led to the convergent evolution of Actinobacteria and some fungi
Similar pressures form the same lifestyle of penetrating and consuming complex organic matter in terrestrial habitats
What leaf-cutter ants gain from symbiotic association with Actinobacteria
Nutrients from leaves they normally wouldn’t be able to break down
What Actinobacteria gain from their symbiotic association with leaf-cutter ants
Protection from fungi and place to live and nutrients
Interactions between a Frankia species and alder plants
Frankia infect alder plant root cells and form nodules where biologically available nitrogen is produced while the plant provides the Frankia with sugars and food
Why infections due to Mycobacterium species are hard to treat
Slow-growing and difficult to culture (antibiotics are rarely used against fast-growing bacteria and slow-growers are less affected by slowing down cell wall synthesis)
How the Mycobacterium membrane is distinct from other bacteria
Form a waxy layer with mycolic acid
A gene sequence that doesn’t produce a protein
Pseudogene
What a high% of pseudogenes in a genome indicates
Indicates host dependence for nutrients and different processes
Propionibacterium species metabolism
Ferment lactic acid (produced by lactic acid bacteria) into propionic acid (primary metabolite) and CO2
Process responsible for the introduction of the diphtheriae toxin into Corynebacterium diphtheria
Lysogenic conversion due to laterial transfer of the toxin gene by the phage
Diphtheriae toxin effect on host cell
Blocks protein synthesis and has degenerative effects on many organs
Morphology of Arthrobacter cell
Pleomorphic
Responsible for the “snapping division” observed when Arthrobacter cells divide
Bent-rod morphology causes rupture on only one side of the cell as the cell grows
Habitat where you would expect to find Cytophaga species
Soil and decaying plant matter, freshwater, and sewage treatment plants
Energy sources used by Cytophaga for metabolism
Degrade macromolecules like DNA, RNA, proteins, cellulose, chitin, and agar
Motility associated with Cytophaga and Flavobacterium species and the surface involved
Gliding motility on solid surface
Habitat where Rhodothermus species may be found
Thermophilic environments like hot springs in marine or freshwater habitats
Habitat of Salinibacter species
High salt environments
Unusual colony morphology of Flavobacterium
Rhizoid/plant-root like
Pigmentation associated with Cytophaga or Flavobacterium
Yellow or orange
Infected by Flavobacterium columnare
Fish
Where Flavobacterium columnare colonize that eventually results in asphyxia
Fish gills
What some marine Flavobacterium use as their energy source
Organic matter produced by algal blooms
When organic matter isn’t available, Flavobacterium use this
Proteorhodopsin
Ortholog to Proteorhodopsin
Bacteriorhodopsin?
Degraded by Bacteroides in the human gut
Plant sugar polymers like cellulose
Environment required by Bacteroides
Obligate anaerobes
2 major contributions of Bacteroides species to humans
Part of a healthy gut microbiome – Catabolize plant material that could be toxic and fermentation products of plant materials can provide up to 15% of the caloric value from food
Causes an increase in the relative abundance of Bacteroides species in the human gut
Eating more plant matter
This phylum decreases in response to increased Bacteroides
Firmicutes
Metabolism and habitat for members of the phylum Chlorobi
Photosynthetic obligate anaerobes that use hydrogen sulfide as a source of electrons; Live below cyanobacteria
Unit that make up the branched archaeal lipids
Isoprenoid
The 2 best described phyla of Archaea
- Crenarchaeota
2. Euryarchaeota
Example of a barophilic hyperthermophile
Pyrodictium abyssi
Example of a double extremophile that grows at 80C and pH 3
Sulfolobus solfataricus
Carbon dioxide and hydrogen gas methanogen reaction
CO2 + 4H2 -> CH4 + 2H2O
Example of syntrophic consortium
An acetogen + a methanogen
Halorhodopsin function
Pumps in Cl-
Detects and moves toward red light
Sensory rhodopsin I
Activated by blue light and initiates a reverse motor
Sensory rhodopsin II
Model Streptomyces species
Streptomyces coelicolor
How lactic acid bacteria make ATP
Substrate-level phosphorylation
