Microbial Diversity Flashcards
What are the 2 ways to describe microbial diversity?
1) Phylogenetic diversity
2) Functional diversity
What are phyla most often based on?
16S rRNA gene sequence
What is functional diversity based on?
Activities microbes carry out
Which is generally the largest phyla of bacteria?
Cyanobacteria
What 3 types of cells are included in the cyanobacteria?
- Unicellular
- Filamentous
- Branching filamentous
Which phyla of bacteria can form heterocysts?
Cyanobacteria
What are heterocysts?
Specialized nitrogen fixing cells
What do heterocysts use to fix nitrogen?
Sunlight
What kind of photosynthesis do cyanobacteria carry out?
Oxygenic
What does oxygenic photosynthesis mean?
Harvest energy from light and produce oxygen
Are cyanobacteria heterotrophs or autotrophs?
Autotrophs
Where do cyanobacteria carry out photosynthesis?
Thylakoids
What are similarities and differences between cyanobacteria and chloroplasts?
- Both carry out photosynthesis in thylakoids
- Cyanobacteria have cell walls; chloroplasts do not
Are cyanobacteria gram positive or negative?
Negative
What can be found in cyanobacteria cell walls?
Peptidoglycan
Where can cyanobacteria be found?
Terrestrial, freshwater, and marine habitats
Which organism has the lowest nutritional requirements?
Cyanobacteria
What organism accounts for about half of the photosynthesis in the world’s oceans?
Prochlorococcus
What kind of organisms are found in the phylum Proteobacteria?
- Chemolithotrophs
- Chemoorganotrophs
- Phototrophs
- Facultative organisms
What are the 6 classes of proteobacteria & how well studied is each class?
- Alpha, Beta, & Gamma are well studied
- Delta & Epsilon are smaller classes known for some “strange” bacteria
- Zeta is barely studied with only one known species
What can be found in the class Alphaproteobacteria?
Pathogens & non-pathogens
What is an example of a non-pathogen found in Alphaproteobacteria and what does it do?
- Rhizobium leguminosarum
- Forms root nodules on legume plants in a symbiotic relationship
What is an example of a pathogen found in Alphaproteobacteria and what does it do?
- Rickettsia rickettsii
- Obligate intracellular pathogen that causes “Rocky Mountain spotted fever”
What is the closest relative to the eukaryotic mitochondria phylogenetically?
Rickettsia
What can be found in Betaproteobacteria?
Pathogens & non-pathogens
What is a example of a non-pathogenic Betaproteobacteria and what does it do?
- Neisseria mucosa
- Lives on mucous membranes of the human body but does not cause harm
What is a pathogenic example of a Betaproteobacteria and what does it do?
- Neisseria gonorrhoeae
- Causes gonnorhea
What is a non-pathogenic example of a Gammaproteobacteria and what does it do?
- Escherichia coli
- Gram negative, rod shapred, facultative aerobe, motile by peritrichous flagella
- Ferments lactose to a mixture of acids and alcohols
- Lives in large intestine of mammals & indicates fecal contamination
What is a pathogenic example of a Gammaproteobacteria and what does it do?
- Pseudomonas aeruginosa
- Gram negative, rod shaped, motile by polar flagella, does not ferment sugars
- Naturally resistant to many antibiotics
- Opportunistic pathogen – causes infections in immunocompromised patients
What bacteria causes respiratory tract infections in cystic fibrosis patients?
Pseudomonas aeruginosa
What is an example of a Deltaproteobacteria and what does it do?
- Myxococcus xanthus
- Gliding motility
- Releases exoenzymes to lyse other bacteria for nutrients
What are firmicutes?
Low GC gram positives
What kind of bacteria are included in firmicutes?
- Lactic acid bacteria – fermentation produces lactic acid as an endproduct
- Non-lactic acid bacteria
What are 2 examples of lactic acid firmicutes and what do they do/what are they used for?
- Lactobacillus delbrueckii – yogurt production
- Streptococcus pyogenes – cause of strep throat, scarlet fever, & the flesh eating disease
What is an example of a non-lactic acid firmicute and what are its characteristics?
- Staphylococcus aureus
- Facultative aerobe that forms grape-like clusters
- Lives on skin
- Halotolerant – can be isolated using media with high NaCl, such as mannitol salt agar
- Cause of nosocomial infections
What are the 2 best studied genera of endospore former’s and are they aerobic or anaerobic?
- Bacillus – aerobic
- Clostridium –strictly anaerobic
Where are endospore formers primarily found?
Soil
What are the majority of soil organisms?
Non-pathogenic saprophytic
What are 2 examples of endospore forming firmicutes and what are they used for?
- Bacillus subtilis used as a model for gram positive cell strcture & cell division and differentiation
- Clostridium botulinum – strict anaerobe with a fermentative metabolism that secretes a variety of exoenzymes to degrade plant material
What do Tenericutes stain in the Gram stain?
Phylogenetically related to Gram positives but don’t have a cell wall so they stain Gram negative
What is an example of a Tenericute and what does it cause?
- Mycoplasma genitalium
- Causes urethritis and pelvic inflammatory disease
What was the first free-living bacterium to have it’s genome sequenced?
Mycoplasma genitalium
Which bacteria has one of the smallest genomes known?
Mycoplasma genitalium
What are Actinobacteria?
High GC Gram positives
What is included in Actinobacteria?
Coryneform bacteria with a “club-shaped” morphology
What is an example of Actinobacteria and what does it cause?
- Corynebacterium diphtheriae
- Produces an endotoxin that inhibits protein synthesis
- Causes tissue death in respiratory tract (diphtheria)
What are 3 characteristics of Mycobacteria?
- Modified Gram positive cell wall
- Layer of mycolic acids outside peptidoglycan
- Makes them acid-fast
What is an example of a Mycobacterium and what are its characteristics?
- Mycobacterium tuberculosis
- Slow growing, can take weeks to grow on agar medium
- Cause of tuberculosis
What are Streptomyces?
Genus of filamentous Gram positives
What do Streptomyces form?
Branching hyphae and mycelia which produce reproductive spores (conidia, NOT ENDOSPORES) for dispersal
What are 3 characteristics of Streptomyces?
- Obligate aerobes
- Live in well aerated soils
- Produce substances that kill or inhibit growth of other microbes
What is an example of Streptomyces and what does it produce?
- Streptomyces griseus
- Produces streptomycin, a broad spectrum protein synthesis inhibitor active against Gram negative bacteria
What are bacteroidetes?
Large, heterogenous phylum of Gram negatives
What are be found in bacteroidetes?
Aerobes & anaerobes
What is an example of a Bacteroidete and what are its characteristics?
- Bacteroides thetaiotaomicron
- Strict anaerobe
- Dominant in human large intestine
- Produces enzymes to degrade polysaccharides, greatly increasing the plant polymers that can be digested in the human gut
What are Chlamydiae?
Gram negatives that lack peptidoglycan
What are characteristics of Chlamydiae?
- Obligate intracellular parasites
- Unique life cycle with 2 types of cells – elementary body and reticulate body
What are characteristics of an elementary body?
- Small dense cell, resists drying
- Allows infection of new host cells
What are characteristics of a reticulate body?
- Larger vegetative cells
- Multiply inside an existing host but are not infective
What is an example of Chlamydiae and what does it cause?
- Chlamydia trachomatis
- Causes trachoma (infection of the eye) through scarring and blindness
What are plantomycetes?
Budding and appendaged bacteria
What is used for attachment in plantomycetes?
Protein “stalk”
What is lacking in plantomycetes cell wall?
Peptidoglycan
What is an example of Plantomycetes and what is 1 characteristic about it?
- Gemmata obscuriglobus
- Nucleoid is surrounded by a true-unit membrane
What may the last universal common ancestor (LUCA) have been?
Hyperthermophilic
What are 2 famous species of Deinococcus-Thermus?
1) Thermus aquaticus
2) Deinococcus radiodurans
What are 4 characteristics of Thermus aquaticus?
- Thermophilic chemoorganoheterotroph
- Source of temperature stable enzymes (Taq DNA polymerase)
- Allows DNA synthesis reactions to be carried out quickly at high temperatures
- Essential tool for PCR (polymerase chain reaction)
What are 4 characteristics of Deinococcus radiodurans?
- Extremely resistant to radiation
- Highly effective DNA repair mechanisms
- Form pairs or tetrads
- Gram negative cell wall but stains Gram positive because of thick peptidoglycan
How many phyla does Archaea have?
5
What are Euryarchaeota?
Extremely halophilic bacteria
What is the key genus of Euryarchaeota?
Halobacterium
What are characteristics of Halobacterium?
- Require high salt concentrations (at least 1.5M or about 9%)
- Found in solar salt evaporation ponds and salt lakes with a salt concentration near saturation
- Need to maintain osmotic balance (usually through accumulation)
- Pump large amounts of K+ into the cell from the environment (higher K+ inside than Na+ outside)
What does Euryarchaeota possess adaptations to?
Life in highly ionic environments
What is a unique feature found in only some haloarchaea?
Light-driven synthesis of ATP using bacteriorhodopsin
What is involved in the light-driven synthesis of ATP?
Cytoplasmic membrane proteins absorb light energy and pump protons across the membrane to make ATP
What are haloarchaea considered when they are capable of light-driven synthesis of ATP and why?
Photoheterotrophs because the cannot fix CO2
What are the key genera of methanogenic Euryarchaeota?
Methanobacterium and methanosarcina
Why were methanogens given their name?
Only microbes capable of significant methane production
What group of archaea produce the bulk of CH4 in the atmosphere?
Methanogens
Are methanogens aerobes or anaerobes?
Strictly anaerobic
What is a similarity and a difference between pseudomurein and peptidoglycan?
- Similar in structure
- Different in composition
What is found in many methanogens?
An S-layer as their cell wall made of protein or glycoprotein
What are common substrates for methanogens?
- H2 + CO2
- Formate
- Acetate
- Methanol
Do all methanogens use the same substrates?
No, some can only use one and not others
What substrates do Methanobacterium use?
H2 + CO2
What substrates does Methanosarcina use?
Acetate & methanol
How can other compounds such as glucose be converted to methane?
Through cooperative reactions between methanogens and other anaerobic bacteria
What is the key genus of Thaumarchaeota?
Nitrosopumilus
What are 3 characteristics of Nitrosopumilus?
- Grows chemolithotrophically by aerobically oxidizing ammonia
- Uses CO2 as only carbon source
- Can grow at very low levels of ammonia
Where are Nitrosopumilus typically found?
In open ocean water where they are key to ammonia oxidation
What is an example of Nanoarchaeota and what are its characteristics?
- Nanoarchaeum equitans
- Obligate symbiont of the crenarchaeote Ignicoccus
- Lacks genes for all but core molecular processes
What is one of the smallest cellular organisms?
Nanoarchaeum equitans
What is an example of Korarchaeota and what are its characteristics?
- Korarchaeum cryptofilum
- Obilagately anaerobic chemoorganotroph
- Hyperthermophile
- Cells are long, thin filaments
- Lack many core genes
What is the habitat of Korarchaeota?
Hot springs
What are characteristics of Crenarchaeota?
- Most are hyperthermophiles; others found in extreme cold environments
- Chemoorganotrophs or chemolithotrophs
- Some can respire aerobically, while others carry out anaerobic respiration
What is an example of Crenarchaeota?
Sulfolobus
What are characteristics of Sulfolobus?
- Grows in sulfur-rich acidic hot springs (pH = 2)
- Aerobic chemolithotrophs that oxidize reduced sulfur or iron
Which genus contains a lot of representatives that have an optimum growth temperature about 100 C?
Crenarchaeota
