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MBIO 1010 > Lecture 7: Prokaryotic Diversity > Flashcards

Lecture 7: Prokaryotic Diversity Flashcards

1
Q

what are the two ways to describe microbial diversity?

A

phylogenetic diversity
functional diversity

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2
Q

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

A

phylogenetic diversity

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3
Q

On the phylogenetic tree, The _____ represent the
phyla only known from
metagenome sequencing
from diverse environmental
samples

A

red dots

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4
Q

The tree includes 92 named
bacterial phyla, 26 archaeal
phyla and all ____ of the
Eukaryotic super groups

A

five

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5
Q

______: Groups microbes based on the activities they carry out

A

functional diversity

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6
Q

T/F: Most prokaryotes have been cultured in the lab

A

false! most cannot (yet)

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6
Q

T/F: when categorizing organisms using functional diversity, some functions appear to be performed in a single phylum only

A

true!

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6
Q

Some are known only from 18S sequences or metagenomic
studies

A

false! known from 16S sequence

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7
Q

T/F: Some phyla are well studied in the lab

A

true!

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8
Q

T/F: Mycoplasmas are phylogenetically related to Gram positives, but they don’t have a cell wall

A

true! can’t be gram stained effectively (will always be negative)

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9
Q

T/F: mycoplasmas are not pleomorphic

A

false! they are

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10
Q

__________: 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

A

Mycoplasma genitalium

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11
Q

T/F: actinobacteria are gram negative

A

False! gram positive

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12
Q

coryneform bacteria (from actinobacteria) have a _____ morphology

A

club-shaped

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13
Q

_______: Produces an exotoxin that inhibits protein synthesis

Causes tissue death in the respiratory tract - diphtheria

Can lead to death by
suffocation

A

Corynebacterium diphtheriae

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14
Q

T/F: Mycobacteria have a modified Gram
positive cell wall

A

true!
Layer of mycolic acids outside the peptidoglycan layer

Makes them acid-fast

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15
Q

Why do mycobacterium have mycolic acid layer outside peptidoglycan layer?

A

makes them acid-fast

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16
Q

_______: Slow growing (~ 24 hr/gen)

Colonies can take weeks to form on agar medium

Cause of tuberculosis – slow, fatal respiratory disease

A

Mycobacterium tuberculosis

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17
Q

_____: Genus of filamentous Gram positives

A

Filamentous Actinobacteria

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18
Q

________: Form branching hyphae and mycelia

A

Filamentous Actinobacteria

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19
Q

what do hyphae produce for dispersal?

A

reproductive spores (conidia)

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20
Q

are conidia produced by filamentous actinobacteria endospores?

A

no!

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21
Q

filamentous actinobacteria are mostly… (aerobic/anaerobic)

so where do they live?

A

obligate aerobes so they live in well aerated soils

Give soil its earthy smell: geosmins

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22
Q

________: Also produce substances that kill or
inhibit the growth of other microbes - antibiotics

A

filamentous actinobacteria

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23
Q

______: Produces streptomycin: broad spectrum protein synthesis inhibitor active against
Gram negative bacteria

A

Streptomyces griseus

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24
Q

Large, heterogeneous phylum of Gram
negative bacteria?

A

Bacteroidetes

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25
Q

T/F: Bacteroidetes are specifically aerobes

A

false, aerobes and anaerobes

dont really have many unifying characteristics as a phylum

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26
Q

_______: 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

A

Bacteroides thetaiotaomicron

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27
Q

Chlamydiae have a gram negative cell wall but lack what?

A

peptidoglycan

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28
Q

_____ are Obligate intracellular parasites

A

chlyamydiae

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29
Q

what are the two types of cells in a chlamydiae life-cycle?

A

elementary body
reticulate body

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30
Q

what is the function of an elementary body for chlamydiae?

A

allows infection of new host cells

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31
Q

what is the function of a reticulate body for chlamydiae?

A

multiply inside existing host

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32
Q

______: Trachoma: infection of the eye

Causes scarring and blindness

A

Chlamydia trachomatis

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33
Q

______: Budding and appendaged bacteria

Protein stalk used for attachment

Lack peptidoglycan in the cell wall

Some have membrane-bound compartments inside the cell

A

Planctomycetes

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34
Q

______: Nuceoid is surrounded by a true unit membrane

A

Gemmata obscuriglobus

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35
Q

_____: Impressive morphological diversity, generally larger than other
bacteria
* Unicellular, filamentous, or branching filamentous

A

Cyanobacteria

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36
Q

what are heterocysts?

A

Specialized nitrogen fixing cells

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37
Q

T/F: All Cyanobacteria carry out oxygenic photosynthesis

A

true

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38
Q

T/F: All Cyanobacteria are heterotrophs

A

false!

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39
Q

what do autotrophs do?

A

Fix CO2 to build cell material- Calvin cycle

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40
Q

Like chloroplasts cyanobacteria carry out photosynthesis in specialized
membranes called ______

A

thylakoids

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41
Q

cyanobacteria are unlike chloroplasts in what way?

A

they have cell walls!

contain peptidoglycan, gram negative cell wall

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42
Q

where can cyanobacteria be found?

A

Widely distributed in terrestrial, freshwater, and marine habitats

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43
Q

T/F: cyanobacteria have the lowest nutritional requirements of any
organisms

A

true! primary producers

44
Q

______: One of the most abundant organisms on
Earth

Accounts for ~ half of photosynthesis in the
World’s oceans

A

Prochlorococcus

45
Q

_______: Includes many of the most commonly
encountered bacteria, and is the most metabolically diverse phylum

A

proteobacteria

46
Q

what are the six classes of proteobacteria?

A

alpha, beta, gamma- well studied and many important species
delta, epsilon- smaller classes with broad range of phenotypes
zeta- only one known species!

47
Q

Mariprofundus ferrooxydans is from which proteobacteria phylum?

A

zetaproteobacteria- the only known species!

48
Q

_____proteobacteria: Includes pathogens and non-pathogens

A

alpha

49
Q

_____proteobacteria: Metabolically diverse

Some are pathogens and some are non-
pathogens

A

beta

50
Q

_____proteobacteria: Metabolically and ecologically diverse
* Many grow well in the lab and have become
important research models

A

gamma

51
Q

_____proteobacteria: Contains many species with strange behavior

A

delta

52
Q

_____proteobacteria: A small class
* Famous for a few microaerophilic,
spirillum shaped pathogens

A

epsilon

53
Q

______: Forms root nodules on
legume plants
* Symbiotic relationship
* Bacterium fixes nitrogen
into a bioavailable form
* Plant provides nutrients and
a home for the bacteria

A

Rhizobium leguminosarum
non-pathogen form of alphaproteobacteria

54
Q

______: Obligate intracellular pathogen
* Carried by insects and transmitted by insect bites
* Causes Rocky Mountain spotted fever
* Phylogenetically _____ is the
closest relative to the eukaryotic mitochondrion

A

Rickettsia rickettsii

55
Q

______: Non-pathogenic commensal of the human body: lives on
mucous membranes

A

Neisseria mucosa

56
Q

______: Pathogenic: causes
gonorrhea

A

Neisseria gonorrhoeae

57
Q

what does commensal mean?

A

doing us no harm, accept it as part of us!

can still do us harm if the immune system isn’t watching though!

58
Q

______: 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

A

Escherichia coli

59
Q

______: 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

A

Pseudomonas aeruginosa

60
Q

______: 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

A

Myxococcus xanthus

61
Q

______: 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 (from periplasm!)

A

Bdellovibrio bacteriovorus

62
Q

______: Frequently transmitted in
under-cooked chicken
* One of the most common
causes of food-borne illness
* Causes gastroenteritis and
bloody diarrhea (means it made it past stomach acid! likely because bacteria were too numerous to neutralize)

A

Campylobacter jejuni

63
Q

T/F: Firmicutes phylum have gram negative cell walls

A

false! gram +

64
Q

if firmicutes bacteria are low GC Gram + bacteria, what are they sensitive to?

A

high heat! not as many H bonds in backbone, sensitive to denaturing at high heat

65
Q

the _____ phylum includes lactic acid bacteria

A

firmicutes

66
Q

firmicutes are _____ that produce lactic acid as an end product of fermentation (aerobe/anaerobe)

A

aerotolerant anaerobes

67
Q

_____: Yogurt production
lactic acid bacteria

A

Lactobacillus delbrueckii

68
Q

______: Cause of strep throat, scarlet fever and the flesh eating disease
lactic acid bacteria

A

Streptococcus pyogenes

69
Q

_______: Facultative aerobe that forms characteristic
grape-like clusters
* Lives on skin
* Halotolerant
* Frequent cause of nosocomial (hospital acquired) infections
non-lactic acid bacteria

A

Staphylococcus aureus

70
Q

______: Normal commensal on skin
non-lactic acid bacteria

A

Staphylococcus epidermidis

71
Q

if a bacteria is a common nosocomial infector (hospital acquired) then it must have a strong tolerance for what?

A

disinfectants/cleaning products/antibiotics

“cowards” because they attack the weak but must be pretty strong to not be eliminated by “sterile” hospital environment

72
Q

what are the two best studied genres of endospore forming Firmicutes?

A

Bacillus– aerobic endospore formers
Clostridium– strictly anaerobic endospore formers

73
Q

Bacillus– _____ endospore formers

A

aerobic

74
Q

Clostridium– strictly ______ endospore formers

A

anaerobic

75
Q

Endospore formers are found primarily in _____

A

soil

76
Q

Most endospore forming firmicutes are _______ saprophytic soil organisms

A

non-pathogenic

77
Q

T/F: oxygen tolerance and environment has no effect on endospore formation

A

true!

78
Q

_______:
Important lab bacterium used as a model for:
* Gram positive cell structure and genetics
* Cell division and differentiation into
endospores

endospore forming firmicutes

A

Bacillus subtilis

79
Q

_______: 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

endospore forming firmicutes

A

Clostridium botulinum

80
Q

Clostridium botulinum is commonly used for what cosmetic procedure?

A

botox! neurotoxin causes targeted paralysis of facial muscles etc.

81
Q

Proper canning procedures must either:

A
  • Reach temp above 120°C to destroy endospores
  • Include enough acid or sugar to prevent germination- make it so hypertonic that spores can’t germinate
82
Q

T/F: Suggests that the last universal common
ancestor (LUCA) may have been a hyperthermophile

A

true!

83
Q

what are the two famous species of hyperthermophilic bacteria?

A

Thermus aquaticus
Deinococcus radiodurans

84
Q

________: 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)

A

thermus aquaticus

85
Q

_______: Extremely resistant to radiation
* Highly effective DNA repair mechanisms
* Forms pairs or tetrads (power in numbers!)
* 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

A

Deinococcus radiodurans

86
Q

T/F: Phylogenetically Archaea are split into four phyla

A

false! five

87
Q

T/F: Breadth of phylogenetic diversity in Archaea is similar to that of the Bacteria and Eukarya

A

true!

88
Q

what are the five phyla of archaea?

A

euryarchaeota
nanoarchaeota
korarchaeota
crenarchaeota
thaumarchaeota

89
Q

euryarchaeota are…

A

extreme halophiles

90
Q

_________:
Absolute requirement for high salt concentrations
* Typically need at least 1.5 M (~9%) NaCl for growth
* Found in solar salt evaporation ponds and salt lakes where the salt concentration approaches saturation
* Ex) Great Salt Lake (Utah), Dead Sea
* Ex) soda lakes (highly alkaline hypersaline lakes)

A

Halobacterium salinarum

91
Q

Haloarchaea fall under which archaea phylum?

A

euryarchaeota

92
Q

how does Halobacterium salinarum adapt to highly ionic environment?

A

pumps large amounts of K+ into the cell from the
environment
* Intracellular K+ concentration exceeds extracellular Na+ concentration
* Water flows into the cell in hypersaline environments

93
Q

Halophiles need to maintain osmotic balance… how do they do this?

A

Usually achieved by accumulation or synthesis of compatible solutes

94
Q

Some haloarchaea (phototrophic) have a unique system for
generating energy: what is it?

A

Light-driven synthesis of ATP without the use of
chlorophylls
* Instead they use a pigment called bacteriorhodopsin!

95
Q

________: Integral membrane protein
* Absorbs light energy and pumps protons
across the membrane to make a PMF (proton motive force)
* PMF is used to generate ATP
* They do not fix CO2
* Ex) Photoheterotrophy

A

Bacteriorhodopsin

96
Q

Only microbes capable of significant methane production: _______

A

Methanogens

97
Q

_______: Produce the bulk of CH4 in the atmosphere
* Important green house gas
* Strict anaerobes, found in many diverse anaerobic environments
* Ex) Cow’s gut; Sewage sludge

A

Methanobacterium

98
Q

T/F: reducing carbon dioxide to methane for energy production by methanogens is slightly better than fermentation, way worse than using oxygen

A

true!

99
Q

which euryarchaeota phylums demonstrate diversity of cell wall chemistries

A

methanogenic

100
Q

Methanobacterium uses what instead of peptidoglycan?

A

pseudomurein, similar in structure less similar in composition

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

101
Q

______ archaea phyla accomplishes nitrification

A

Thaumarchaeota

101
Q

______: Aerobic, ammonia oxidizing chemolithoautotroph:
* Converts NH3 into NO2-
for energy
* Uses CO2 for carbon
* Abundant in open ocean water where they seem to be a major player in
nitrogen cycling

A

Nitrosopumilus maritimus

102
Q

why is nitrogen cycling super important in open ocean water?

A

because ocean is not nutrient-rich!

103
Q

________: One of the smallest cellular organisms (~0.4 µm)
* Obligate parasite of the crenarchaeote Ignicoccus (hunt other archaea!)
* Contains one of the smallest genomes known
* Lacks genes for all but core molecular processes
* Depends upon host for most of its cellular needs

from nanoarchaeota phylum

A

Nanoarchaeum equitans

104
Q

________: Obligately anaerobic chemoorganotroph
* Hyperthermophile
* Cells are long, thin filaments
* Lacks many core genes
* Depends on other members of hot springs community and cannot yet be
grown in pure culture
from koraarchaeota phylum

A

Korarchaeum cryptofilum

105
Q

Most ______ (archaea phylum) are hyperthermophiles

A

crenarchaeota

Found in extremely hot environments:
* Boiling hot springs, deep ocean vents

Other representatives are found in extremely cold environments

106
Q

most ______ (archaea phylum) are Chemoorganotrophs or
chemolithotrophs

And most use _____ in their metabolism

A

crenarchaeota
sulfur

107
Q

________: Grows in sulfur-rich acidic hot springs (~90°C, pH 2)
* Hyperthermophile and acidophile
* Aerobic chemolithotroph (reduces oxygen) that oxidizes reduced
sulfur or iron

A

Sulfolobus acidocaldarius

MBIO 1010 (12 decks)

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