Microbial Diversity

Question 1

What are the two ways to describe microbial diversity?

Answer 1

1. Phylogenetic Diversity
2. Functional Diversity

Question 2

1. Phylogenetic Diversity

Answer 2

• Microbes are grouped into phyla based on evolutionary relationships
• Most often based on 16S rRNA gene sequence

Question 3

2. Functional Diversity

Answer 3

• Groups microbes based on the activities they carry out
  
  • Ex. Anoxygenic phototrophs: dispersed through several Phyla

Question 4

Tenericutes (Bacteria Phyla)

Answer 4

• The Mycoplasmas
• Phylogenetically related to Gram positives, but they don’t have a cell wall
  
  • Gram stain 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

Question 5

Actinobacteria (Bacterial Phyla)

Answer 5

• Second phylum of Gram positive bacteria – high GC Gram positives
• Includes coryneform bacteria
  
  • Club-shaped morphology
• Example: Corynebacterium diphtheriae
  
  • Produces an exotoxin that inhibits protein synthesis
  • Causes tissue death in the respiratory tract - diphtheria
  • Can lead to death by suffocation
• Propionic Acid Bacteria
  
  • Swiss Cheese

Question 6

Actinobacteria (Bacterial Phyla) Part 2

Answer 6

• Mycobacteria have a modified Gram positive cell wall
  
  • Layer of mycolic acids outside the peptidoglycan layer
  • Makes them acid-fast (pink)
• Example:
  
  • Mycobacterium tuberculosis
  • Slow growing (~ 24 hr/gen)
  • Colonies can take weeks to form on agar medium
  • Cause of tuberculosis – slow, fatal respiratory disease

Question 7

Filamentous Actinobacteria (Bacterial Phyla)

Answer 7

• Genus of filamentous Gram positives
• Form branching hyphae and mycelia
• Hyphae produce reproductive spores for dispersal – conidia
  
  • Not endospores

Question 8

Filamentous Actinobacteria (Bacterial Phyla) Part 2

Answer 8

• Most are obligate aerobes
• Live in well aerated soils
  
  • Give soil its earthy smell: geosmins
• Also produce substances that kill or inhibit the growth of other microbes - antibiotics
• Example
  
  • Streptomyces griseus
  • Produces streptomycin: broad spectrum protein synthesis inhibitor active against Gram negative bacteria

Question 9

Bacteroidetes (Bacterial Phyla)

Answer 9

• Large, heterogeneous 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 plant polymers that can be digested in the human gut

Question 10

Acidobacteria

Answer 10

• very little is known about acidobacteria
• Only recognized within the last 20 years
• Difficult to cultivate
• First sequenced genome in 2009
• Makes up between 20-50% of soil microbial community

Question 11

Chlamydiae (Bacterial Phyla)

Answer 11

• Gram negative cell wall type, but lack peptidoglycan
• Obligate intracellular parasites
• Unique life-cycle with two types of cells:
  1. Elementary body
  
  • Small dense cell, resists drying
  • Allows infection of new host cells

Question 12

Chlamydiae (Bacterial Phyla) Part 2

Answer 12

2. Reticulate body
   
   • Larger vegetative cells
   • Multiply inside an existing host
   • Are not infective
     - Example: Chlamydia trachomatis
   • Trachoma: infection of the eye
   • Causes scarring and blindness

Question 13

Planctomycetes (Bacterial Phyla)

Answer 13

• Budding and appendaged bacteria
• Protein stalk used for attachment
• Lack peptidoglycan in the cell wall
• Some have membrane-bound compartments inside the cell
  
  • Example: Gemmata obscuriglobus
    
    • Nucleoid is surrounded by a true unit membrane

Question 14

Cyanobacteria (Bacterial Phyla)

Answer 14

• Impressive morphological diversity, generally larger than other bacteria:
  
  • Unicellular, filamentous, or branching filamentous
• Some form heterocysts
  
  • Specialized nitrogen fixing cells

Question 15

Cyanobacteria (Bacterial Phyla) Part 2

Answer 15

• All Cyanobacteria carry out oxygenic photosynthesis
  
  • Harvest energy from light, and produce oxygen
• All are autotrophs
  
  • Fix CO2 to build cell material- Calvin cycle
• Like chloroplasts they carry out photosynthesis in specialized membranes called thylakoids
• Unlike chloroplasts they have cell walls:
  
  • Contain peptidoglycan
  • Gram negative cell wall type

Question 16

Cyanobacteria (Bacterial Phyla) Part 3

Answer 16

• Widely distributed in terrestrial, freshwater, and marine habitats
• Lowest nutritional requirements of any organisms
  
  • Primary producers
• Example: Prochlorococcus
  
  • One of the most abundant organisms on
    Earth
  • Accounts for ~ half of photosynthesis in the
    World’s oceans

Question 17

Proteobacteria (Bacterial Phyla)

Answer 17

• 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

Question 18

Proteobacteria (Bacterial Phyla) Part 2

Answer 18

• Divided into 6 classes:
  
  • Alpha-, Beta-, Gamma-, are well studied with many important species
  • Delta-, Epsilon- are smaller classes but with a broad range of phenotypes
  • Zetaproteobacteria has barely been studied with only one known species:
    
    • Mariprofundus
    • Ferrooxydans

Question 19

Alphaproteobacteria

Answer 19

• Includes pathogens and non-pathogens
  
  • Example of a non-pathogen:
    
    • Rhizobium leguminosarum
      
      • Forms root nodules on legume plants
      • Symbiotic relationship
      • Bacterium fixes nitrogen into a bioavailable form
      • Plant provides nutrients and a home for the bacteria

Question 20

Alphaproteobacteria (Part 2)

Answer 20

• Example of a pathogen:
  
  • Rickettsia rickettsii
  • 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

Question 21

Betaproteobacteria

Answer 21

• Metabolically diverse
• Some are pathogens and some are non-pathogens
  
  • Examples:
    
    • Neisseria mucosa
      
      • Non-pathogenic commensal of the human body: lives on mucous membranes
    • Neisseria gonorrhoeae
      
      • Pathogenic: causes
        gonorrhea

Question 22

Gammaproteobacteria

Answer 22

• Metabolically and ecologically diverse
• Many grow well in the lab and have become important research models
• Examples:
  
  • Escherichia coli
    
    • Gram negative, rod shaped, facultative aerobes
      
      • 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

Question 23

Gammaproteobacteria (Part 2)

Answer 23

• Pseudomonas aeruginosa
  
  • Gram negative, rod shaped, motile by means of polar flagella
    
    • 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

Question 24

Deltaproteobacteria

Answer 24

• Contains many species with strange behavior
  
  • Example: Myxococcus xanthus
    
    • Gliding motility
    • Predatory: releases exoenzymes to lyse other bacteria for nutrients
    • When starved the cells migrate together to forms complex multicellular fruiting bodies
      
      • Individual cells differentiate into myxospores for dispersal

Question 25

Myxococcus Xanthus

Answer 25

• Have 2 forms of motility Adventurous (A) and Social (S)
• Appear to travel in “waves”
• They develop fruiting bodies in response to starvations
• Change from vegetative rod cells into myxospores

Question 26

Deltaproteobacteria (Part 2)

Answer 26

• Ex) Bdellovibrio bacteriovorus
• Curved, highly motile predator of other Proteobacteria and Gram negative bacteria
• Penetrates the cell wall and
  multiplies in the periplasm
• Parasitic: uses macromolecules obtained directly from the host

Question 27

Deltaproteobactera

Answer 27

• Desulfovibrio
• Sulfate reducers
• Obligately anaerobic
• Some play a role in “oil well souring”

Question 28

Epsilonproteobacteria

Answer 28

• A small class
• Famous for a few microaerophilic, spirillum shaped pathogens
• Example:
  
  • Campylobacter jejuni
    
    • Frequently transmitted in under-cooked chicken
    • One of the most common causes of food-borne illness
    • Causes gastroenteritis and bloody diarrhea

Question 29

Firmicutes (Bacterial Phyla)

Answer 29

• One of two phyla with Gram positive cell walls
  
  • Low GC Gram positives
• Includes lactic acid bacteria
  
  • Aerotolerant anaerobes that produce lactic acid as an end product of fermentation
  • Examples
    
    • Lactobacillus delbrueckii
      
      • Yogurt production
    • Streptococcus pyogenes
      
      • Cause of strep throat, scarlet fever and the flesh eating disease

Question 30

Firmicutes (Bacterial Phyla) Part 2

Answer 30

• Includes many non-lactic acid bacteria
  
  • Example
    
    • Staphylococcus aureus
      
      • Facultative aerobe that forms characteristic
        grape-like clusters
      • Lives on skin
      • Halotolerant
        
        • Can be isolated using media with high
          NaCl (Ex: mannitol salt agar): produces acids-yellow
      • Frequent cause of nosocomial infections
    • Staphylococcus epidermidis
      
      • Normal commensal on skin
        
        • Can be distinguished on mannitol salts agar: no acid production-pink

Question 31

Firmicutes (Bacterial Phyla) Part 3

Answer 31

• Endospore forming Firmicutes
• The best studied genera of endospore formers are:
  
  • Bacillus – aerobic endospore formers
  • Clostridium – strictly anaerobic endospore formers
• Endospore formers are found primarily in soil
• Most are non-pathogenic saprophytic soil organisms
  
  • Some can be dangerous pathogens

Question 32

Firmicutes (Bacterial Phyla) Part 4

Answer 32

-Examples:
- Bacillus subtilis
- Important lab bacterium used as a model for:
- Gram positive cell structure and genetics
- Cell division and differentiation into
endospores

Question 33

Firmicutes (Bacterial Phyla) Part 5

Answer 33

• Example: Clostridium botulinum
  
  • 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
    
    • When consumed causes botulism
  • Proper canning procedures must either:
    
    • Reach temp above 120°C to destroy endospores
    • Include enough acid or sugar to prevent germination

Question 34

Hyperthermophilic Bacteria

Answer 34

• There are several deeply branching phyla that consist of hyperthermophilic bacteria
  
  • Suggests that the last universal common ancestor (LUCA) may have been a hyperthermophile

Question 35

What are the 2 famous species of Hyperthermophilic Bacterias?

Answer 35

1. Thermus aquaticus
2. Deinococcus radiodurans

Question 36

Thermus aquaticus

Answer 36

• A thermophilic chemoorganoheterotroph
• 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 polymerase chain reaction (PCR)

Question 37

Deinococcus radiodurans

Answer 37

• Extremely resistant to radiation
  
  • Highly effective DNA repair mechanisms
• Forms pairs or tetrads
• In response to massive DNA damage nucleoids from two cells can fuse to facilitate repair
• Has a Gram negative cell wall type but stains Gram positive because of thick
  peptidoglycan