Lecture 7: Prokaryotic Diversity Flashcards
what are the two ways to describe microbial diversity?
phylogenetic diversity
functional diversity
_______: Microbes are grouped into phyla based on
evolutionary relationships
* Most often based on 16S
rRNA gene sequence
phylogenetic diversity
On the phylogenetic tree, The _____ represent the
phyla only known from
metagenome sequencing
from diverse environmental
samples
red dots
The tree includes 92 named
bacterial phyla, 26 archaeal
phyla and all ____ of the
Eukaryotic super groups
five
______: Groups microbes based on the activities they carry out
functional diversity
T/F: Most prokaryotes have been cultured in the lab
false! most cannot (yet)
T/F: when categorizing organisms using functional diversity, some functions appear to be performed in a single phylum only
true!
Some are known only from 18S sequences or metagenomic
studies
false! known from 16S sequence
T/F: Some phyla are well studied in the lab
true!
T/F: Mycoplasmas are phylogenetically related to Gram positives, but they don’t have a cell wall
true! can’t be gram stained effectively (will always be negative)
T/F: mycoplasmas are not pleomorphic
false! they are
__________: 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
Mycoplasma genitalium
T/F: actinobacteria are gram negative
False! gram positive
coryneform bacteria (from actinobacteria) have a _____ morphology
club-shaped
_______: Produces an exotoxin that inhibits protein synthesis
Causes tissue death in the respiratory tract - diphtheria
Can lead to death by
suffocation
Corynebacterium diphtheriae
T/F: Mycobacteria have a modified Gram
positive cell wall
true!
Layer of mycolic acids outside the peptidoglycan layer
Makes them acid-fast
Why do mycobacterium have mycolic acid layer outside peptidoglycan layer?
makes them acid-fast
_______: Slow growing (~ 24 hr/gen)
Colonies can take weeks to form on agar medium
Cause of tuberculosis – slow, fatal respiratory disease
Mycobacterium tuberculosis
_____: Genus of filamentous Gram positives
Filamentous Actinobacteria
________: Form branching hyphae and mycelia
Filamentous Actinobacteria
what do hyphae produce for dispersal?
reproductive spores (conidia)
are conidia produced by filamentous actinobacteria endospores?
no!
filamentous actinobacteria are mostly… (aerobic/anaerobic)
so where do they live?
obligate aerobes so they live in well aerated soils
Give soil its earthy smell: geosmins
________: Also produce substances that kill or
inhibit the growth of other microbes - antibiotics
filamentous actinobacteria
______: Produces streptomycin: broad spectrum protein synthesis inhibitor active against
Gram negative bacteria
Streptomyces griseus
Large, heterogeneous phylum of Gram
negative bacteria?
Bacteroidetes
T/F: Bacteroidetes are specifically aerobes
false, aerobes and anaerobes
dont really have many unifying characteristics as a phylum
_______: 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
Bacteroides thetaiotaomicron
Chlamydiae have a gram negative cell wall but lack what?
peptidoglycan
_____ are Obligate intracellular parasites
chlyamydiae
what are the two types of cells in a chlamydiae life-cycle?
elementary body
reticulate body
what is the function of an elementary body for chlamydiae?
allows infection of new host cells
what is the function of a reticulate body for chlamydiae?
multiply inside existing host
______: Trachoma: infection of the eye
Causes scarring and blindness
Chlamydia trachomatis
______: Budding and appendaged bacteria
Protein stalk used for attachment
Lack peptidoglycan in the cell wall
Some have membrane-bound compartments inside the cell
Planctomycetes
______: Nuceoid is surrounded by a true unit membrane
Gemmata obscuriglobus
_____: Impressive morphological diversity, generally larger than other
bacteria
* Unicellular, filamentous, or branching filamentous
Cyanobacteria
what are heterocysts?
Specialized nitrogen fixing cells
T/F: All Cyanobacteria carry out oxygenic photosynthesis
true
T/F: All Cyanobacteria are heterotrophs
false!
what do autotrophs do?
Fix CO2 to build cell material- Calvin cycle
Like chloroplasts cyanobacteria carry out photosynthesis in specialized
membranes called ______
thylakoids
cyanobacteria are unlike chloroplasts in what way?
they have cell walls!
contain peptidoglycan, gram negative cell wall
where can cyanobacteria be found?
Widely distributed in terrestrial, freshwater, and marine habitats
T/F: cyanobacteria have the lowest nutritional requirements of any
organisms
true! primary producers
______: One of the most abundant organisms on
Earth
Accounts for ~ half of photosynthesis in the
World’s oceans
Prochlorococcus
_______: Includes many of the most commonly
encountered bacteria, and is the most metabolically diverse phylum
proteobacteria
what are the six classes of proteobacteria?
alpha, beta, gamma- well studied and many important species
delta, epsilon- smaller classes with broad range of phenotypes
zeta- only one known species!
Mariprofundus ferrooxydans is from which proteobacteria phylum?
zetaproteobacteria- the only known species!
_____proteobacteria: Includes pathogens and non-pathogens
alpha
_____proteobacteria: Metabolically diverse
Some are pathogens and some are non-
pathogens
beta
_____proteobacteria: Metabolically and ecologically diverse
* Many grow well in the lab and have become
important research models
gamma
_____proteobacteria: Contains many species with strange behavior
delta
_____proteobacteria: A small class
* Famous for a few microaerophilic,
spirillum shaped pathogens
epsilon
______: Forms root nodules on
legume plants
* Symbiotic relationship
* Bacterium fixes nitrogen
into a bioavailable form
* Plant provides nutrients and
a home for the bacteria
Rhizobium leguminosarum
non-pathogen form of alphaproteobacteria
______: 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
Rickettsia rickettsii
______: Non-pathogenic commensal of the human body: lives on
mucous membranes
Neisseria mucosa
______: Pathogenic: causes
gonorrhea
Neisseria gonorrhoeae
what does commensal mean?
doing us no harm, accept it as part of us!
can still do us harm if the immune system isn’t watching though!
______: 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
Escherichia coli
______: 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
Pseudomonas aeruginosa
______: 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
______: 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!)
Bdellovibrio bacteriovorus
______: 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)
Campylobacter jejuni
T/F: Firmicutes phylum have gram negative cell walls
false! gram +
if firmicutes bacteria are low GC Gram + bacteria, what are they sensitive to?
high heat! not as many H bonds in backbone, sensitive to denaturing at high heat
the _____ phylum includes lactic acid bacteria
firmicutes
firmicutes are _____ that produce lactic acid as an end product of fermentation (aerobe/anaerobe)
aerotolerant anaerobes
_____: Yogurt production
lactic acid bacteria
Lactobacillus delbrueckii
______: Cause of strep throat, scarlet fever and the flesh eating disease
lactic acid bacteria
Streptococcus pyogenes
_______: Facultative aerobe that forms characteristic
grape-like clusters
* Lives on skin
* Halotolerant
* Frequent cause of nosocomial (hospital acquired) infections
non-lactic acid bacteria
Staphylococcus aureus
______: Normal commensal on skin
non-lactic acid bacteria
Staphylococcus epidermidis
if a bacteria is a common nosocomial infector (hospital acquired) then it must have a strong tolerance for what?
disinfectants/cleaning products/antibiotics
“cowards” because they attack the weak but must be pretty strong to not be eliminated by “sterile” hospital environment
what are the two best studied genres of endospore forming Firmicutes?
Bacillus– aerobic endospore formers
Clostridium– strictly anaerobic endospore formers
Bacillus– _____ endospore formers
aerobic
Clostridium– strictly ______ endospore formers
anaerobic
Endospore formers are found primarily in _____
soil
Most endospore forming firmicutes are _______ saprophytic soil organisms
non-pathogenic
T/F: oxygen tolerance and environment has no effect on endospore formation
true!
_______:
Important lab bacterium used as a model for:
* Gram positive cell structure and genetics
* Cell division and differentiation into
endospores
endospore forming firmicutes
Bacillus subtilis
_______: 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
Clostridium botulinum
Clostridium botulinum is commonly used for what cosmetic procedure?
botox! neurotoxin causes targeted paralysis of facial muscles etc.
Proper canning procedures must either:
- 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
T/F: Suggests that the last universal common
ancestor (LUCA) may have been a hyperthermophile
true!
what are the two famous species of hyperthermophilic bacteria?
Thermus aquaticus
Deinococcus radiodurans
________: 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)
thermus aquaticus
_______: 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
Deinococcus radiodurans
T/F: Phylogenetically Archaea are split into four phyla
false! five
T/F: Breadth of phylogenetic diversity in Archaea is similar to that of the Bacteria and Eukarya
true!
what are the five phyla of archaea?
euryarchaeota
nanoarchaeota
korarchaeota
crenarchaeota
thaumarchaeota
euryarchaeota are…
extreme halophiles
_________:
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)
Halobacterium salinarum
Haloarchaea fall under which archaea phylum?
euryarchaeota
how does Halobacterium salinarum adapt to highly ionic environment?
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
Halophiles need to maintain osmotic balance… how do they do this?
Usually achieved by accumulation or synthesis of compatible solutes
Some haloarchaea (phototrophic) have a unique system for
generating energy: what is it?
Light-driven synthesis of ATP without the use of
chlorophylls
* Instead they use a pigment called bacteriorhodopsin!
________: 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
Bacteriorhodopsin
Only microbes capable of significant methane production: _______
Methanogens
_______: 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
Methanobacterium
T/F: reducing carbon dioxide to methane for energy production by methanogens is slightly better than fermentation, way worse than using oxygen
true!
which euryarchaeota phylums demonstrate diversity of cell wall chemistries
methanogenic
Methanobacterium uses what instead of peptidoglycan?
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
______ archaea phyla accomplishes nitrification
Thaumarchaeota
______: 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
Nitrosopumilus maritimus
why is nitrogen cycling super important in open ocean water?
because ocean is not nutrient-rich!
________: 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
Nanoarchaeum equitans
________: 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
Korarchaeum cryptofilum
Most ______ (archaea phylum) are hyperthermophiles
crenarchaeota
Found in extremely hot environments:
* Boiling hot springs, deep ocean vents
Other representatives are found in extremely cold environments
most ______ (archaea phylum) are Chemoorganotrophs or
chemolithotrophs
And most use _____ in their metabolism
crenarchaeota
sulfur
________: Grows in sulfur-rich acidic hot springs (~90°C, pH 2)
* Hyperthermophile and acidophile
* Aerobic chemolithotroph (reduces oxygen) that oxidizes reduced
sulfur or iron
Sulfolobus acidocaldarius
