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Microbiology > 4A. Microbial Diversity - Bacteria > Flashcards

4A. Microbial Diversity - Bacteria 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

Phylogenetic diversity

A
  • grouped into phyla based on evolutionary relationships
  • based on 16s rRNA gene sequence
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3
Q

Explain this tree

A

Red dots - phyla only known from metagenome sequencing from diverse environmental samples

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4
Q

Functional diversity

A
  • Groups microbes based on the activities they carry out
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5
Q

How are function and phylum different?

A
  • Phylo doesn’t tell alot about function
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6
Q

Examples of functional diversity on many phylums vs only 1 phylum

A

Many: anoxygenic phototrophs - dispersed through several phyla
1: oxygenic phototroph - cyanobacteria

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7
Q

Summarize this photo and general take aways

A
  • most prokaryotes cannot be cultured in the lab yet
  • some can be studied in a lab (green)
  • some are only known based on 16s sequence or metagenomic studies (red)
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8
Q

Tenericutes (phylum) - species example, gram, defining features

A
  • species: Mycoplasmas
  • phylogenetically (16s rRNA) related to gram positives
  • they gram stain negative tho - no cell wall
  • not gram negative or postiive
  • pleomorphic: can change shape or no defined shape
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9
Q

Ex of Tenericute (phylum) and defining features

A

mycoplasma genitalium (species)
- common cause of urethritis and pid
- first-free living bacteria to have it’s genome sequenced

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10
Q

Actinobacteria (phylum) - gram, 3 genus examples

A
  • high GC gram positive (3 bonds)
  • ex:
    1. Corynebacterium
    2. Mycobacteria
    3. Filamentous
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11
Q

2 species examples of actinobacteria (phylum)

A
  1. Corynebacterium diphtheriae (species): produces an exotoxin that inhibits protein synthesis - causes tissue death in the respiratory tract - can lead to death by suffocation
  2. propionic acid bacteria - makes swiss cheese
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12
Q

mycobacteria (genus) - gram, defining features and ex

A
  • modified gram positive cell wall - layer of mycolic acids outside peptidoglycan layer (Makes them acid fast)
    ex) mycobacterium tuberculosis (slow growing - colonies can take weeks to form on agar medium)
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13
Q

Filamentous actinobacteria (genus) - defining features

A
  • genus of filamentous gram positives
  • form branching hyphae and mycelia
  • hyphae produce reproductive spores for dispersal (conidia)
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14
Q

Is conidia an endospore?

A

NO!

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15
Q

filamentous actinobacteria (genus) and oxygen

A
  • most are obligate aerobes
  • live in well aerated soils
  • gives soil the earthy smell (geosmins)
  • produce substances that kill or inhibit the growth of other microbes (antibiotics)
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16
Q

Ex of obligate filamentous bacteria (genus) + defining features

A
  • streptomyces griseus (species)
  • produces streptomycin - broad spectrum protein synthesis inhibitor active against gram negative bacteria
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17
Q

Cons of broad spectrum antibiotic

A

also kills good bacteria since it kills everything

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18
Q

Competitive exclusion

A

good microbes take up space so bad bacteria can’t

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19
Q

Bacteroidetes (phylum) - gram, defining features

A
  • large, heterogenous phylum of gram negative bacteria
  • aerobes and anaerobes
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20
Q

ex of bacteroidetes (phylum) + defining features

A

bacteroides thetaiotaomicron (species)
- strict anaerobe
- in the human large intestine
- enzymes to degrade polysaccharides - increases the variety of plant polymers that can’t be digested in the human gut

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21
Q

acidobacteria (phylum) - defining features

A
  • very little is known
  • makes up 20-50% of soil microbial community
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22
Q

chlamydiae (phylum) - gram, defining features

A
  • gram negative cell wall type (lack peptidoglycan)
  • obligate intracellular parasites
  • unique life-cycle with 2 types of cells - elementary and reticulate
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23
Q

2 types of bodies in chlamydiae (phylum)

A
  1. elementary body
    - small, dense cells that resist drying
    - allows infection of new host cells
    - metabollically inactive (dormant)
  2. reticulate body
    - large vegetative cells
    - multiply inside an existing hose
    - not infective
    - living
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24
Q

ex of chlamydiae (phylum) + defining features

A

chlamydia trachomatis (species)
- infection of the eye

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25
Q

fill in the blanks

A
26
Q

Planctomycetes (phylum) - defining features

A
  • budding and appendages bacteria
  • protein stalk is used for attachment
  • lack peptidoglycan in cell wall
  • some have membrane-bound compartments inside the cell
27
Q

ex of planctomycetes (phylum)

A

gemmata obscuriglobus (species)
- nucleiod is surrounded by a true unit membrane

28
Q

in planctomyces what is and isnt an appendage

A

appendage: stalk
not: flagellum and pilus

29
Q

cyanobacteria (phylum) - defining features

A
  • impressive morphological diversity
  • generally larger than other bacteria
  • unicellular, filamentous or branching filamentous
  • some form heterocysts - specialized nitrogen fixing cells
30
Q

What do all cyanobacteria carry out and where

A
  • they all carry out oxygenic photosynthesis - harvest energy from light and produce oxygen
  • all are autotrophs - fix CO2 to build cell material
  • photosynthesis is in thylakoids
31
Q

do cyanobacteria have cell walls

A

yes! with peptidoglycan and gram negative cell wall

32
Q

example of cyanobacteria (phylum)

A

prochlorococcus (genus)
- half of photosynthesis in the worlds oceans

33
Q

where can you find cyanobacteria and what are their growth requirements

A
  • widely distributed in terrestrial, freshwater and marine habitats
  • lowest nutritional requirements since they’re primary producers but still need all 10
34
Q

toxic blooms - phylum and defining feature

A

cyanobacteria
- produce toxins that effect nervous system

35
Q

proteobacteria (phylum) + defining features

A
  • most commonly encountered
  • chemolithotrophs, chemoorganotrophs, phototrophs, facultative organisms (switch from 1 metabolic lifestyle to another)
36
Q

6 classes of proteobacteria (phylum) and how common they are

A
  • these are all genus
    alpha, beta, gamma - most common
    delta, epsilon - smaller range
    zeta - barely known
37
Q

alphaprotebacteria (genus) - defining feature

A

includes pathogens and non-pathogens

38
Q

ex of alphaproteobacteria that is a nonpathogen + defining features

A

rhizobium leguminosarum (species)
- forms root nodules on legume plants
- symbiotic relationship
- bacterium fixes nitrogen into a bioavailable form
- plant provides nutrients and a home for the bacteria

39
Q

ex of alphaproteobacteria that is a pathogen + defining features

A

rickettsia rickettshii (species)
- obligate intracellular pathogen
- carried and transmitted by insects
- causes rocky mountain fever
- closest relative to mitochondrion

40
Q

betaproteobacteria (genus) + defining features

A
  • metabolically diverse
  • includes pathogens and non-pathogens
41
Q

ex of betaproteobacteria that is a pathogen and nonpathogen + defining features

A
  • both species:
    non: neisseria mucosa - lives on mucus membranes
    pathogen: neisseria gonorrhoeae - causes gonorrhea
42
Q

gammaproteobacteria (genus) + defining features

A
  • metabollically and ecologically diverse
  • many grow well in a lab and are important research models
43
Q

ex of 2 gammaproteobacteria + defining features

A
  1. e. coli (species)
    - gram negative, rod shaped, facultative aerobes
    - motile by peri-flagella
    - ferments lactose to a mixture of acids and alcohol
    - resident of the large intestine of warm-blooded animals
    - important indicator of fecal contamination
  2. pseudomonas aeruginosa (species)
    - gram negative, rod shaped
    - motile by polar-flagella
    - doesnt ferments lactose
    - resistant to many antibiotics and disinfectants
    - opportunistic pathogen - causes infection in immunocompromised patients
44
Q

ex of opportunistic pathogens

A

respiratory tract infections in cystic fibrosis patients

45
Q

ex of deltaproteobacteria (genus) + defining features

A

myxococcus xanthus
- gliding motility
- predatory: releases exoenzymes to lyse other bacteria for nutrients
- when starved the cells migrate together to form complex multicellular fruiting bodies
- individual cells differentiate into myxospores for dispersals (NOT ENDOSPORES)

46
Q

whats stronger - endospore or myxospores

A

endospores

47
Q

2 forms of motility of myxococcus xanthus

A
  1. adventurous - single cells can distribute/explore
  2. social - single cells don’t move but cells close together will move eachother
    - travel in waves
    - develop fruiting bodies in response to starvation
    - change from vegetative rod cells into myxospores
48
Q

bdellovibrio bacteriovorus (species) - what genus, defining features

A
  • deltaproteobacteria
  • curved, highly motile predator of other proteobacteria and gram negative bacteria
  • preys on cells like e.coli
  • penetrates the cell wall and multiplies in the periplasm
  • small so it can fit in periplasm
  • parasitic: uses macromolecules obtained directly from host
  • uses multiple fission - elongates and divides into a bunch of other cells
49
Q
A
50
Q

deltaproteobacteria and oxygen

A
  • sulfate reducers
  • obligately anaerobic
51
Q

epsilonproteobacteria (genus) + defining feature

A
  • famous for a few microaerophilic spirillum shaped pathogens
52
Q

ex of epsilonproteobacterium (genus) + defining features

A

campylobacter jejuni
- basically like salmonella in chicken

53
Q

firmicutes (phylum) - gram, defining features

A

-gram positive cell walls
- low GC gram positives

54
Q

ex of firmicutes (phylum) - lactic acid bacteria (genus) + defining features

A
  • aerotolerant anaerobes that produce lactic acid as an end product of fermentation
  • lactobacillus delbrueckii (yogurt) - species
  • streptomyces pyogenee (strep throat) - species
55
Q

2 ex of firmicutes (phylum) - non-lactic acid bacteria (genus) + defining features

A
  1. staphylococcus aureus (species)
    - facultative aerobe that forms grape-like clusters
    - lives on skin
    - halotolerant
    - acid production - yellow on mannitol salt plate
    - causes nosocomial infections (infection from hospital)
  2. staphylococcus epidermidis (species
    - normal on skin
    - no acid production - pink on mannitol salt plate
56
Q

endospores and firmicutes

A
  • bacillus - aerobic endospore formers
  • clostridium - strictly anaerobic endospore formers
  • found in soil
  • non-pathogenic saprophyitic (decomposer) soil organisms
57
Q

what is bacillus subtilis (species) used as a model for + genus

A
  • genus: firmicutes
  • important for lab bacterium
  • gram positive cell structure and genetics
  • cell division and differentiation into endospores
58
Q

clostridium botulinum (species) - phylum, oxygen, location, defining features

A
  • phylum: firmicutes
    oxygen: strict anaerobe with a fermentative metabolism
    location: lives in tiny anoxic pockets in soil - can grow in anaerobic canned foods
    function:
    1. secretes exoenzymes to degrade plant material
    2. produces a deadly neurotoxin - causes botulism
59
Q

proper canning procedures

A
  • reach temp above 120 to destroy endospores
  • include enough acid or sugar to prevent germination
60
Q

what could luca be and why

A

hyperthermophilic bacteria because of the deep brances

61
Q

2 hyperthermophilic bacteria species + defining features

A
  1. thermus aquaticus (chemoorganoheterotroph)
    - source of temperature stable enzymes - taq polymerase
    - allows DNA synthesis reactions in the lab to be carried out quickly at high temps
    - needed for PCR
  2. deinococcus radiodurans
    - resistant to radiation
    - highly effective DNA repair mechanisms
    - to repair mutations from radiation
    - forms pairs or tetrads
    - in response to massive DNA damage nucleoids from 2 cells can fuse to facilitate repair
    - has gram negative cell wall type but stains gram positive because of this peptidoglycan

Microbiology (8 decks)

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