4A. Microbial Diversity - Bacteria Flashcards
What are the two ways to describe microbial diversity?
- phylogenetic diversity
- functional diversity
Phylogenetic diversity
- grouped into phyla based on evolutionary relationships
- based on 16s rRNA gene sequence
Explain this tree
Red dots - phyla only known from metagenome sequencing from diverse environmental samples
Functional diversity
- Groups microbes based on the activities they carry out
How are function and phylum different?
- Phylo doesn’t tell alot about function
Examples of functional diversity on many phylums vs only 1 phylum
Many: anoxygenic phototrophs - dispersed through several phyla
1: oxygenic phototroph - cyanobacteria
Summarize this photo and general take aways
- 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)
Tenericutes (phylum) - species example, gram, defining features
- 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
Ex of Tenericute (phylum) and defining features
mycoplasma genitalium (species)
- common cause of urethritis and pid
- first-free living bacteria to have it’s genome sequenced
Actinobacteria (phylum) - gram, 3 genus examples
- high GC gram positive (3 bonds)
- ex:
1. Corynebacterium
2. Mycobacteria
3. Filamentous
2 species examples of actinobacteria (phylum)
- 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
mycobacteria (genus) - gram, defining features and ex
- 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)
Filamentous actinobacteria (genus) - defining features
- genus of filamentous gram positives
- form branching hyphae and mycelia
- hyphae produce reproductive spores for dispersal (conidia)
Is conidia an endospore?
NO!
filamentous actinobacteria (genus) and oxygen
- 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)
Ex of obligate filamentous bacteria (genus) + defining features
- streptomyces griseus (species)
- produces streptomycin - broad spectrum protein synthesis inhibitor active against gram negative bacteria
Cons of broad spectrum antibiotic
also kills good bacteria since it kills everything
Competitive exclusion
good microbes take up space so bad bacteria can’t
Bacteroidetes (phylum) - gram, defining features
- large, heterogenous phylum of gram negative bacteria
- aerobes and anaerobes
ex of bacteroidetes (phylum) + defining features
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
acidobacteria (phylum) - defining features
- very little is known
- makes up 20-50% of soil microbial community
chlamydiae (phylum) - gram, defining features
- gram negative cell wall type (lack peptidoglycan)
- obligate intracellular parasites
- unique life-cycle with 2 types of cells - elementary and reticulate
2 types of bodies in chlamydiae (phylum)
- 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
ex of chlamydiae (phylum) + defining features
chlamydia trachomatis (species)
- infection of the eye
fill in the blanks
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
ex of planctomycetes (phylum)
gemmata obscuriglobus (species)
- nucleiod is surrounded by a true unit membrane
in planctomyces what is and isnt an appendage
appendage: stalk
not: flagellum and pilus
cyanobacteria (phylum) - defining features
- impressive morphological diversity
- generally larger than other bacteria
- unicellular, filamentous or branching filamentous
- some form heterocysts - specialized nitrogen fixing cells
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
do cyanobacteria have cell walls
yes! with peptidoglycan and gram negative cell wall
example of cyanobacteria (phylum)
prochlorococcus (genus)
- half of photosynthesis in the worlds oceans
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
toxic blooms - phylum and defining feature
cyanobacteria
- produce toxins that effect nervous system
proteobacteria (phylum) + defining features
- most commonly encountered
- chemolithotrophs, chemoorganotrophs, phototrophs, facultative organisms (switch from 1 metabolic lifestyle to another)
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
alphaprotebacteria (genus) - defining feature
includes pathogens and non-pathogens
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
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
betaproteobacteria (genus) + defining features
- metabolically diverse
- includes pathogens and non-pathogens
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
gammaproteobacteria (genus) + defining features
- metabollically and ecologically diverse
- many grow well in a lab and are important research models
ex of 2 gammaproteobacteria + defining features
- 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 - 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
ex of opportunistic pathogens
respiratory tract infections in cystic fibrosis patients
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)
whats stronger - endospore or myxospores
endospores
2 forms of motility of myxococcus xanthus
- adventurous - single cells can distribute/explore
- 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
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
deltaproteobacteria and oxygen
- sulfate reducers
- obligately anaerobic
epsilonproteobacteria (genus) + defining feature
- famous for a few microaerophilic spirillum shaped pathogens
ex of epsilonproteobacterium (genus) + defining features
campylobacter jejuni
- basically like salmonella in chicken
firmicutes (phylum) - gram, defining features
-gram positive cell walls
- low GC gram positives
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
2 ex of firmicutes (phylum) - non-lactic acid bacteria (genus) + defining features
- 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) - staphylococcus epidermidis (species
- normal on skin
- no acid production - pink on mannitol salt plate
endospores and firmicutes
- bacillus - aerobic endospore formers
- clostridium - strictly anaerobic endospore formers
- found in soil
- non-pathogenic saprophyitic (decomposer) soil organisms
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
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
proper canning procedures
- reach temp above 120 to destroy endospores
- include enough acid or sugar to prevent germination
what could luca be and why
hyperthermophilic bacteria because of the deep brances
2 hyperthermophilic bacteria species + defining features
- 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 - 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
