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Microbial Diversity Flashcards

1
Q

What are the two ways to describe microbial diversity?

A
  1. Phylogenetic Diversity
  2. Functional Diversity
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2
Q
  1. Phylogenetic Diversity
A
  • Microbes are grouped into phyla based on evolutionary relationships
  • Most often based on 16S rRNA gene sequence
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3
Q
  1. Functional Diversity
A
  • Groups microbes based on the activities they carry out
    • Ex. Anoxygenic phototrophs: dispersed through several Phyla
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4
Q

Tenericutes (Bacteria Phyla)

A
  • 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
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5
Q

Actinobacteria (Bacterial Phyla)

A
  • 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
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6
Q

Actinobacteria (Bacterial Phyla) Part 2

A
  • 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
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7
Q

Filamentous Actinobacteria (Bacterial Phyla)

A
  • Genus of filamentous Gram positives
  • Form branching hyphae and mycelia
  • Hyphae produce reproductive spores for dispersal – conidia
    • Not endospores
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8
Q

Filamentous Actinobacteria (Bacterial Phyla) Part 2

A
  • 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
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9
Q

Bacteroidetes (Bacterial Phyla)

A
  • 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
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10
Q

Acidobacteria

A
  • 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
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11
Q

Chlamydiae (Bacterial Phyla)

A
  • 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
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12
Q

Chlamydiae (Bacterial Phyla) Part 2

A
  1. 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
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13
Q

Planctomycetes (Bacterial Phyla)

A
  • 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
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14
Q

Cyanobacteria (Bacterial Phyla)

A
  • Impressive morphological diversity, generally larger than other bacteria:
    • Unicellular, filamentous, or branching filamentous
  • Some form heterocysts
    • Specialized nitrogen fixing cells
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15
Q

Cyanobacteria (Bacterial Phyla) Part 2

A
  • 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
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16
Q

Cyanobacteria (Bacterial Phyla) Part 3

A
  • 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
17
Q

Proteobacteria (Bacterial Phyla)

A
  • 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
18
Q

Proteobacteria (Bacterial Phyla) Part 2

A
  • 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
19
Q

Alphaproteobacteria

A
  • 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
20
Q

Alphaproteobacteria (Part 2)

A
  • 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
21
Q

Betaproteobacteria

A
  • 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
22
Q

Gammaproteobacteria

A
  • 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
23
Q

Gammaproteobacteria (Part 2)

A
  • 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
24
Q

Deltaproteobacteria

A
  • 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
25
Q

Myxococcus Xanthus

A
  • 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
26
Q

Deltaproteobacteria (Part 2)

A
  • 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
27
Q

Deltaproteobactera

A
  • Desulfovibrio
  • Sulfate reducers
  • Obligately anaerobic
  • Some play a role in “oil well souring”
28
Q

Epsilonproteobacteria

A
  • 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
29
Q

Firmicutes (Bacterial Phyla)

A
  • 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
30
Q

Firmicutes (Bacterial Phyla) Part 2

A
  • 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
31
Q

Firmicutes (Bacterial Phyla) Part 3

A
  • 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
32
Q

Firmicutes (Bacterial Phyla) Part 4

A

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

33
Q

Firmicutes (Bacterial Phyla) Part 5

A
  • 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
34
Q

Hyperthermophilic Bacteria

A
  • There are several deeply branching phyla that consist of hyperthermophilic bacteria
    • Suggests that the last universal common ancestor (LUCA) may have been a hyperthermophile
35
Q

What are the 2 famous species of Hyperthermophilic Bacterias?

A
  1. Thermus aquaticus
  2. Deinococcus radiodurans
36
Q

Thermus aquaticus

A
  • 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)
37
Q

Deinococcus radiodurans

A
  • 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

MBIO 1010 (13 decks)

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