4A. Microbial Diversity - Bacteria Flashcards
(61 cards)
1
Q
What are the two ways to describe microbial diversity?
A
- phylogenetic diversity
- functional diversity
2
Q
Phylogenetic diversity
A
- grouped into phyla based on evolutionary relationships
- based on 16s rRNA gene sequence
3
Q
Explain this tree
A
Red dots - phyla only known from metagenome sequencing from diverse environmental samples
4
Q
Functional diversity
A
- Groups microbes based on the activities they carry out
5
Q
How are function and phylum different?
A
- Phylo doesn’t tell alot about function
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
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)
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
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
10
Q
Actinobacteria (phylum) - gram, 3 genus examples
A
- high GC gram positive (3 bonds)
- ex:
1. Corynebacterium
2. Mycobacteria
3. Filamentous
11
Q
2 species examples of actinobacteria (phylum)
A
- Corynebacterium diphtheriae (species): produces an exotoxin that inhibits protein synthesis - causes tissue death in the respiratory tract - can lead to death by suffocation
- propionic acid bacteria - makes swiss cheese
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)
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)
14
Q
Is conidia an endospore?
A
NO!
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)
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
17
Q
Cons of broad spectrum antibiotic
A
also kills good bacteria since it kills everything
18
Q
Competitive exclusion
A
good microbes take up space so bad bacteria can’t
19
Q
Bacteroidetes (phylum) - gram, defining features
A
- large, heterogenous phylum of gram negative bacteria
- aerobes and anaerobes
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
21
Q
acidobacteria (phylum) - defining features
A
- very little is known
- makes up 20-50% of soil microbial community
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
23
Q
2 types of bodies in chlamydiae (phylum)
A
- elementary body
- small, dense cells that resist drying
- allows infection of new host cells
- metabollically inactive (dormant) - reticulate body
- large vegetative cells
- multiply inside an existing hose
- not infective
- living
24
Q
ex of chlamydiae (phylum) + defining features
A
chlamydia trachomatis (species)
- infection of the eye
25
fill in the blanks
26
Planctomycetes (phylum) - defining features
- budding and appendages bacteria
- protein stalk is used for attachment
- lack peptidoglycan in cell wall
- some have membrane-bound compartments inside the cell
27
ex of planctomycetes (phylum)
gemmata obscuriglobus (species)
- nucleiod is surrounded by a true unit membrane
28
in planctomyces what is and isnt an appendage
appendage: stalk
not: flagellum and pilus
29
cyanobacteria (phylum) - defining features
- impressive morphological diversity
- generally larger than other bacteria
- unicellular, filamentous or branching filamentous
- some form heterocysts - specialized nitrogen fixing cells
30
What do all cyanobacteria carry out and where
- 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
do cyanobacteria have cell walls
yes! with peptidoglycan and gram negative cell wall
32
example of cyanobacteria (phylum)
prochlorococcus (genus)
- half of photosynthesis in the worlds oceans
33
where can you find cyanobacteria and what are their growth requirements
- widely distributed in terrestrial, freshwater and marine habitats
- lowest nutritional requirements since they're primary producers but still need all 10
34
toxic blooms - phylum and defining feature
cyanobacteria
- produce toxins that effect nervous system
35
proteobacteria (phylum) + defining features
- most commonly encountered
- chemolithotrophs, chemoorganotrophs, phototrophs, facultative organisms (switch from 1 metabolic lifestyle to another)
36
6 classes of proteobacteria (phylum) and how common they are
- these are all genus
alpha, beta, gamma - most common
delta, epsilon - smaller range
zeta - barely known
37
alphaprotebacteria (genus) - defining feature
includes pathogens and non-pathogens
38
ex of alphaproteobacteria that is a nonpathogen + defining features
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
ex of alphaproteobacteria that is a pathogen + defining features
rickettsia rickettshii (species)
- obligate intracellular pathogen
- carried and transmitted by insects
- causes rocky mountain fever
- closest relative to mitochondrion
40
betaproteobacteria (genus) + defining features
- metabolically diverse
- includes pathogens and non-pathogens
41
ex of betaproteobacteria that is a pathogen and nonpathogen + defining features
- both species:
non: neisseria mucosa - lives on mucus membranes
pathogen: neisseria gonorrhoeae - causes gonorrhea
42
gammaproteobacteria (genus) + defining features
- metabollically and ecologically diverse
- many grow well in a lab and are important research models
43
ex of 2 gammaproteobacteria + defining features
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
ex of opportunistic pathogens
respiratory tract infections in cystic fibrosis patients
45
ex of deltaproteobacteria (genus) + defining features
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
whats stronger - endospore or myxospores
endospores
47
2 forms of motility of myxococcus xanthus
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
bdellovibrio bacteriovorus (species) - what genus, defining features
- 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
50
deltaproteobacteria and oxygen
- sulfate reducers
- obligately anaerobic
51
epsilonproteobacteria (genus) + defining feature
- famous for a few microaerophilic spirillum shaped pathogens
52
ex of epsilonproteobacterium (genus) + defining features
campylobacter jejuni
- basically like salmonella in chicken
53
firmicutes (phylum) - gram, defining features
-gram positive cell walls
- low GC gram positives
54
ex of firmicutes (phylum) - lactic acid bacteria (genus) + defining features
- aerotolerant anaerobes that produce lactic acid as an end product of fermentation
- lactobacillus delbrueckii (yogurt) - species
- streptomyces pyogenee (strep throat) - species
55
2 ex of firmicutes (phylum) - non-lactic acid bacteria (genus) + defining features
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
endospores and firmicutes
- bacillus - aerobic endospore formers
- clostridium - strictly anaerobic endospore formers
- found in soil
- non-pathogenic saprophyitic (decomposer) soil organisms
57
what is bacillus subtilis (species) used as a model for + genus
- genus: firmicutes
- important for lab bacterium
- gram positive cell structure and genetics
- cell division and differentiation into endospores
58
clostridium botulinum (species) - phylum, oxygen, location, defining features
- 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
proper canning procedures
- reach temp above 120 to destroy endospores
- include enough acid or sugar to prevent germination
60
what could luca be and why
hyperthermophilic bacteria because of the deep brances
61
2 hyperthermophilic bacteria species + defining features
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
