Booklet 4: Microbial Diversity Flashcards
List the 2 ways to describe microbial diversity
- Phylogenetic diversity
- Functional diversity
Describe phylogenetic diversity
- Microbes are grouped into phyla based on evolutionary relationships
- Most often based on 16S rRNA gene sequence
Describe functional diversity
Groups microbes based on the activities they carry out.
Example: an oxygenic phototrophs
List 6 points about cyanobacteria
- Impressive morphological diversity, generally larger than other bacteria: unicellular, filamentous, or branching filaments.
- Some form heterocysts (specialized nitrogen fixing cells)
- All cyanobacteria carry out oxygenic photosynthesis
- All are autotrophs (fix CO2 to build cell material
- Carry out photosynthesis in specialized membranes called thylakoids
- Unlike chloroplasts, they have cell walls which contain peptidoglycan and a have a gram negative cell wall type.
Where are cyanobacteria widely distributed?
In terrestrial, freshwater, and marine habitats
T or F: Cyanobacteria have the highest nutritional requirements of any organisms
False - they have the lowest nutritional requirements of any organism. They are known as primary producers.
What is an example of a cyanobacteria?
Prochlorococcus
- One of the most abundant organisms on earth
- Accounts for half of photosynthesis in the world’s oceans.
Describe Proteobacteria
- Includes many of the most commonly encountered bacteria
- Most metabolically diverse phylum
- chemolithotrophs
- chemoorganotrophs
- phototrophs
- facultative organisms that can switch from one metabolic lifestyle to another
Proteobacteria are divided into 6 classes. What are they?
- Alpha - well studied
- Beta - well studied
- Gamma - well studied
- Delta - mostly known for strange bacteria
- Epsilon - mostly known for strange bacteria
- Zetaproteobacteria - has barely been studied with only one known species
What does alphaproteobacteria include?
Pathogens and non-pathogens
What is an example of a non-pathogen within alphaproteobacteria?
Rhizobium leguminosarum:
-forms root nodules on legume plants which is a symbiotic relationship
Describe a symbiotic relationship
- bacterium fixes nitrogen into a bioavailable form
- plant provides nutrients and home for the bacteria
What is an example of a pathogen within alphaproteobacteria?
Rickettsia rickettsi:
- Obligate intracellular pathogen
- Carried by insects and transmitted by insect bites
- Causes Rocky Mountain spotted fever
- Phylogenetically, Rickettsia is the closest relative to the eukaryotic mitochondrion
What does facultative mean?
It can switch from one form of metabolism to another (anaerobic or aerobic) in order to survive.
T or F: Betaprotobacteria have both non-pathogens and pathogens.
True - they are quite metabolically diverse
What is an example of betaprotobacteria?
Neisseria mucosa:
-it is a non-pathogenic commensal of the human body and it lives on mucous membranes
Neisseria gonorrhoea:
-pathogenic - causes the STI of gonorrhoea
What is an example of gammaproteobacteria? Describe it.
E. coli:
- gram negative, rod shaped, facultative aerobe, motile by means of peritrichous flagella
- ferments lactose to a mixture of acids and alcohols
- resident of the large intestine of warm-blooded animals
- serves as an important indicator of fecal contamination
What is another example of gammaproteobacteria? Describe it.
Pseudomonas aeruginosa:
- gram negative, rod shaped, motile by means of polar flagella, but does not ferment sugars
- naturally resistant to many antibiotics and disinfectants
- opportunistic pathogen (causes infections in immunocompromised patients - ex: respiratory tract infections in cystic fibrosis patients)
What is an example of deltaproteobacteria? Describe it.
Myxococccus xanthus:
- gliding motility
- predatory - releases exoenzymes to lyse other bacteria for nutrients
- when starved these cells migrate together to form complex multicellular fruiting bodies
- individual cells differentiate into myxospores for dispersal
Describe firmicutes
- one of two phyla with gram positive cell walls
- low GC (low guanine and cytosine - means it’s less temperature stable)
- gram positives
- includes lactic acid bacteria - fermentation produces lactic acid as an end product
List and describe 3 examples of firmicutes
- Lactobacillus delbreuckii:
- involved in yogurt production - Streptococcus pyogenes
- cause strep through, scarlet fever and the flesh eating disease - Staphylococcus aureus
- facultative aerobe that forms characteristic grape-like clusters
- lives on skin
- halotolerant - can be isolated using media with high NaCl like a mannitol salt agar
- frequent cause of nosocomial (hospital) infections
What are the two best studied genera of endospore formers?
- Bacillus - aerobic endospore formers
- Clostridium - strictly anaerobic endospore formers
Where are endospores primarily found?
In the soil
T or F: Most endospore forming firmicutes are pathogenic saprophytic soil organisms.
False - most on non-pathogenic however some can be dangerous pathogens
Describe Bacillus subtilis (an endospore forming firmicute)
Important lab bacterium used as a model for:
- gram positive cell structure and genetics
- cell division and differentiation (into endospores)
Describe Clostridium botulinum (an endospore forming firmicute)
- strict anaerobe with a fermentative metabolism
- lives in tiny anoxic pockets in the soil
- secretes a variety of exoenzymes to degrade plant material
- can also grow in anaerobic canned foods
- produces a deadly neurotoxin which wen consumed causes botulism
What do proper canning procedures to prevent getting botulism include?
- Reach temp above 120 degrees C
- Or, include enough acid or sugar to prevent germination
What are Tenericutes: the Mycoplasmas?
What is an example? Describe it.
-Phylogenetically related to gram positives but they don’t have a cell wall so they stain gram negative
-Often pleomorphic
Example: Mycoplasma genitalium
-common cause of urethritis and pelvic inflammatory disease
-first free-living bacterium to have it’s genome sequenced
-one of the smallest genomes known at 500 kbp
What are Actinobacteria?
- second phylum of gram positive bacteria
- high GC (high guanine and cytosine - means it’s more temperature stable)
- gram positive
Provide and describe an example of an Actinobacterium?
Corynebacterium diphtheriae:
- club shaped morphology
- produces an exotoxin that inhibits protein synthesis
- causes tissue death in the respiratory tract (diphtheria)
- can lead to death by suffocation
Mycobacteria are also a division of Actinobacteria. Describe them.
-Mycobacteria have a modified gram positive cell wall
-Layer of mycelia acids outside the peptidoglycan layer which makes them acid fast
Ex: Mycobacterium tuberculosis
-slow growing
-colonies can take weeks to form on agar medium
-cause of tuberculosis which is a slow fatal respiratory disease
Streptomycin are a type of filamentous Acintobactera. Describe them.
-genus of filamentous gram positives
-form branching hyphae and mycelia
-hyphae produce reproductive spores for dispersal known as CONIDIA
NOTE: conidia are not endospores!!
-most are obligate aerobes
-live in well aerated soils
-also produce substances that kill of inhibit the growth of other microbes (antibiotics)
What gives soil it’s earthy smell?
Geosmins
What are bacteroidetes? Provide an example
-large, heterogenous phylum of gram negative bacteria
-aerobes and anaerobes
-few unifying characteristics
Example: Bacteroides thetaiotaomicron
-strict anaerobe
-numerically dominant microbe in the human large intestine
-produces enzymes to degrade polysaccharides, greatly increasing the variety of plan polymers that can be digested in the human gut
What are chlamydiae?
- gram negative cell wall type, but lack peptidoglycan
- obligate intracellular parasites
- unique life-cycle with two types of cells: elementary body and reticulate body
Describe the elementary body of chlamydiae.
- small dense cell, resists drying
- allows infection of new host cells
Describe the reticulate body of chlamydiae.
- larger vegetative cells
- multiply inside an existing host but are not infective
What is an example of chlamydiae?
Trachoma (infection of the eye)
-causes scarring and blindness
Describe planctomycetes
- budding and appendages bacteria
- protein “stalk” used for attachment
- lack peptidoglycan in the cell wall
- some have membrane-bound compartments inside the cell
What is an example of a plantomycete?
Gemmata obscuriglobus:
-nucleoid is surrounded by a true-unit membrane
What suggests that the last universal common ancestor (LUCA) may have been a hyperthermophile?
There are several deeply branching phyla that consist of hyperthermophilic bacteria
What are the two famous specious of hyper thermophilic bacteria?
- Thermus aquaticus
- Deinococcus radiodurans
List 4 points about Thermus aquaticus
- A thermophilic chemoorganohereotroph
- Source of temperature stable enzymes - Taq DNA polymerase
- Allows DNA synthesis reactions in the lab to be carried out quickly at high temperatures
- An essential tool for PCR (polymerase chain reaction)
List 4 points about deinococcus radiodurans
- Extremely resistant to radiation
- Highly effective DNA repair mechanisms
- Forms paris or tetrads. In response to massive DNA damage, can fuse nucleotides from two cells to facilitate repair
- Has a gram negative cell wall type, but stains gram positive because of thick peptidoglycan
Phylogenetically, how many phyla are Archaea slit into? List them.
Five:
- Euryarchaeota
- Nanoarchaeota
- Korarchaeota
- Crenarchaeota
- Thaumarchaeota
Euryarchaeota are extremely halophilic Archaea. They are known as Haloarchaea. Describe their nutritional requirements and where they can be found.
Key genus: Halobacterium
- Have a requirement for high salt concentrations
- Typically require at least 1.5 M (9%) NaCl for growth
- Found in solar salt evaporation ponds, and salt lakes where the salt concentration approaches saturation
- Also found in Great Salt Lake (Utah), Dead Sea, as well as Soda Lakes that are highly alkaline hyper saline environments
Describe the water balance of halophilic archaea.
- Halophiles need to maintain osmotic balance
- This is usually achieved by accumulation or synthesis of compatible solutes
- Halobacterium species instead pump large amounts of K+ into the cell from the environment.
- Intracellular K+ concentration exceeds extracellular Na+ concentration and positive water balance is maintained
What is a unique feature found in only some haloarchaea? Describe it.
- Light-driven synthesis of ATP using bacteriorhodopsin (the reason cells are pink).
- Cytoplasmic membrane proteins that can absorb light energy and pump protons across the membrane to make ATP
- Cannot fix CO2
- Therefore, they are photoheterotrophs!
What are the 2 key generas of Euryarchaeota: Methanogenic Archaea? Describe them.
-Methanobacterium
-Methanosarcina
They are termed Methanogens because they are the only microbes capable of significant methane production.
They produce the bulk of CH4 in the atmosphere.
They are strict anaerobes. Ex: cow’s gut, sewage sludge
What is pseudomurein?
- A similar structure to peptidoglycan
- Only the Methanobacteriales family has this type of cell wall
- Most other types of methanogens have a S-layer made of protein or glycoprotein as their cell wall.
What are examples of substrates that obligate aerobes use?
H2 + CO2, formate, acetate, methanol
What is the key genus of Thaumarchaeota?
List some points about it.
Nitrosopumilus :
- grows chemolithotrophically by aerobically oxidizing ammonia
- uses CO2 as it’s only carbon source
- can grow at very low levels of ammonia
- indigenous to open ocean water where they are a major player in ammonia oxidation
What is an example of Nanoarchaeota?
Nanoarchaeum equitans:
-Obligate symbiont of the crenarchaeote Ignicoccus
What is an example of Korarchaeota?
Korarchaeum cryptofilum:
- obligately anaerobic chemoorganotroph
- hyperthermophile
- cells are long, thin filaments
Describe Crenarhaeota
- Most are hyperthermophiles (Found in extreme heat environments)
- Other representatives are found in extreme cold environments
- Chemoorganotrophs or chemolithotrophs
What is an example of Crenarchaeota?
Sulfolobus:
- grows in sulphur-rich acidic hot springs
- aerobic chemolithotrophs that oxidize reduced sulphur or iron
