1. Phylogenetic Diversity

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

2. Functional Diversity

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

- 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

Microbial Diversity Flashcards by Sophia Matulis Zerbinato

What are the two ways to describe microbial diversity?

Phylogenetic Diversity
Functional Diversity

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Phylogenetic Diversity

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

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Functional Diversity

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

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Tenericutes (Bacteria Phyla)

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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Actinobacteria (Bacterial Phyla)

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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Actinobacteria (Bacterial Phyla) Part 2

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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Filamentous Actinobacteria (Bacterial Phyla)

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

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Filamentous Actinobacteria (Bacterial Phyla) Part 2

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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Bacteroidetes (Bacterial Phyla)

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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Acidobacteria

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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Chlamydiae (Bacterial Phyla)

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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Chlamydiae (Bacterial Phyla) Part 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

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Planctomycetes (Bacterial Phyla)

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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Cyanobacteria (Bacterial Phyla)

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

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Cyanobacteria (Bacterial Phyla) Part 2

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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Cyanobacteria (Bacterial Phyla) Part 3

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

Proteobacteria (Bacterial Phyla)

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 (Bacterial Phyla) Part 2

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

Alphaproteobacteria

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

Alphaproteobacteria (Part 2)

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

Betaproteobacteria

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

Gammaproteobacteria

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

Gammaproteobacteria (Part 2)

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

Deltaproteobacteria

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

Myxococcus Xanthus

- 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

Deltaproteobacteria (Part 2)

- 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

Deltaproteobactera

- Desulfovibrio - Sulfate reducers - Obligately anaerobic - Some play a role in "oil well souring"

Epsilonproteobacteria

- 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

Firmicutes (Bacterial Phyla)

- 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

Firmicutes (Bacterial Phyla) Part 2

- 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

Firmicutes (Bacterial Phyla) Part 3

- 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

Firmicutes (Bacterial Phyla) Part 4

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

Firmicutes (Bacterial Phyla) Part 5

- 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

Hyperthermophilic Bacteria

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

What are the 2 famous species of Hyperthermophilic Bacterias?

1. Thermus aquaticus 2. Deinococcus radiodurans

Thermus aquaticus

- 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)

Deinococcus radiodurans

- 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