block B - bacteria Flashcards
what is the difference between gram positive and negative bacteria?
gram negative bacteria have a thin peptidoglycan wall with an outer membrane made of lipopolysaccharide whereas gram positive bacteria haven’t got an outer membrane but they do have far thicker layers of peptidoglycan membranes
what are the 5 classes of proteobacteria?
alpha-
beta-
delta-
gamma-
epsilon-
how many described species are there of alphaproteobacteria?
nearly 1000
what are the 6 major orders of alphaproteobacteria?
Rhizobiales
Rickettsiales
Rhodobacterales
Rhodospirillales
Caulobacterales
Sphingomonadales
what are magnetospirillum?
they are members of alphaproteobacteria, gammaproteobacteria, deltaproteobacteria and nitrospira
theyre magnetomatic, demonstrating directed movement in a magentic feild
how many described species of betaproteobacteria are there?
500
what are the 6 major orders of betaproteobacteria?
Burkholderiales
Hydrogenophilales
Methylophilales
Niesseriales
Nitrosomonadales
Rhodocyclales
what are zooglea?
Chemoorganotroph that produces thick capsule
Important in wastewater treatment
what does meningococcus meningitidis cause?
meningitis
what is chromobacteria?
they’re rod-shaped, facultative aerobe
some species produce pigment violacein
what is nitrification caused by? and why is it very important?
nitrosomonas + nitrobacter = nitrification
this is very important in managing ammonia
what does the key genus of methophylus do?
it is obligate and facultative methylotrophs
what are methyltrophs?
they are a large group of microorganisms that can reduce one-carbon compounds like methanol
what do nitrosomonadales do? and what is their key genus?
their key genus is nitrosomonas and they are obligate chemolithotrophic ammonia oxidisers
what are hydrogenophilales and what is their key genus?
key genus: hydrogenophylus, thiobacillus and hydrogenophylus
they are obligate aerobes that can grow as chemolithotrophs
another key genus: thiobacillus
these are obligate aerobes that can be chemolithophilic or chemoorganotroph
what are the key genera of enteribacteriales?
enterobacter, escherichia, klebsiella, proteus, salmonella, shigella and serratia
are enteric becteria and enterobacteriales the same thing?
yes they are
what nutritional requirements for enteric bacteria are there?
they have relatively simple nutritional requirements
what are enterobacteriales?
they are a phylogenetic group in gammaproteobacteria
they are facultative anaerobes which can be motile or nonmotile, with nonsporulating rods
they can ferment sugar to a variety of end products
what are the two groups that enteric bacteria can be split into by the type and proportion of fermentation of glucose?
mixed-acid fermenters
2,3-butandieol fermenters
what is the structure if escheriachia coli?
they are straight rods which are Peritrichously flagellate (they have flagella evenly distributed around them) or theyre non-motile
what is the distribution of Escherichia coli determined by?
the presence in the bowel of humans and animals - presence in water indicative of RECENT faecal contamination
what are the types of microorganisms in the mixed-acid fermenters category?
escherichia
salmonella and shigella
what is erishchia?
thyere universal inhabitants of the intstinal tract of humans and warm-blooded animals - they su=ynthesus vitamins for the host
some strains are pathogenic
what are salmonella and shingella?
they are closely related to erisherichia and are usually pathogenic
salmonella is charachetrised immunologically by surface antigens
how many strains of e. coli are there?
over 700
what are the differenet antigens derived from?
O antigens- derived from the cell wall
H antigens - derived from the flagella and only found in motile strains
K antigens- derived from polysaccharide capsules secreted by the organism
why is E. coli perhaps the most studies living organism?
becuase its an essential member of EVERY molecular biology and biochemistry lab
it has applications in biotechnology: recombinant proteins, biofuels and synthetic biology ect.
theyre also easy to grow- 37 degrees with a doubling time of 30 mins and theyre metabolically diverse
what are butanediol fermenters?
theyre a very closely related group of organisms
enteriobacteria are under this category, as are klebsiella
where are enterobacteria found? what may they cause?
in water, sewage and the intestinal tract of humans and warm blooded animals
they may cause urinary tract infections
where are klebisella found? and what do they do? and what is the name of the strain that causes pneumonia?
in soil and water
most strains fix nitrogen and klebsiella pneumoniae occasionally causes pneumonia
what are pseudomonades?
they are chemoorganotrophs which can use a wide variety of organic compounds
they can be oxidase-positive and catalase-positive
they can cause animal and plant diseases
what types of infections can P. aeruginosa cause for individuals who are predisposed?
ketatitis (eyes), diabetic foot ulcers, burns, cystic fibrosis and COPD
what are vibrionales?
they are oxidative-positive curved rods which are fermentative
what facts do you know about vibrio spp.?
theyre generally aquatic
some of the research interest about them is because theyre symbiotic with animals
theyre gram negative
they have curved bacilli, gamma subdivision of the proteobacteria, polar flagella
oxidase positive
what happens when vibrio spp. bind to the gut wall?
they adhere to the gut wall and secrete a toxin that causes devastating diarrheoa
complex of 1 A and 5 B subunits. B adgeres to intestinal epithelial cells, A is translocated into the hist cell, all of this activates adenylyl cyclase leading to >cAMP levels
this all leads to ion imbalance and diarrhoea
‘rice water’ stool
the rate of water loss is higher than can be replaced
what are the key bacteria of deltaproteobacteria?
Bdellovibrio, Myxococcus, Desulfovibrio, Geobacter, Syntrophobacter
what do deltaproteobacteria do?
they are sulphate and sulphur reducers
dissimative iron reducers
bacterial preditors
what are the key genera of Epsilonproteobacteria?
Key genera: Campylobacter, Helicobacter
Campylobacter and Helicobacter and sulfurospirillum
what are Epsilonproteobacteria?
they are gram-negative, motile spirilla oxidase- and catalase- positive
pathogenic to humans and animals
what are sulphospirillum?
theyre not pathogenic, free-living microaerophils that carry out anerobic respiration
what happens if your infected with campylobacter? - [basically how long is the incubation period, what are the clinical features, what is the transmission, what is the reservoir and what causes large outbreaks of this]
the incubation period is 1-11 days (usually 2-5 days)
the clinical features are abdominal pain, diarrhoea, lalaise
the reservoir is the GI tract of birds and animals, cattle and pets
transmission- raw/uncooked meat (especially poultry), unpasteurized milk, bird-pecked milk on doorsteps, untreated water and domestic pets with diarrhoea
person-to-person if personal hygine is poor
the infective dose is really low but it doesnt multiply in food so foodbourne outbreaks are rare
Large outbreaks from raw and inadequately pasteurised milk and contaminated water supplies. Occupational exposure when processing poultry in abattoirs may be implicated in some cases.
what are the 4 phyla that make up more than 90% of characterised genera and species?
proteobacteria
actinobacteria
firmicutes
bacteroidetes
what are gram-positive cell walls made up of?
they can contain up to 90% peptidoglycan, its common to have teichoic acids embedded in their cell wall
what are lipotechoic acids?
theyre teichoic acids covalently bound to membrane lipids
what does morphology mean?
it means cell shape
what are the major cell morphologies?
coccus- spherical or ovoid
rod- cylindrical shape
spirillum - spiral shape
what are some cells with unusual shapes?
spirochetes, appendaged bacteria and filamentous bacteria
what produces the shape of the bacteria?
where the peptoglycan is added to the cell walls is how the shape forms
what are the major gram-positive bacterial groups?
actinobacteria- coryneform bacteria, mycobacterium, filamentous actinobacteria: streptomyces
tenericutes- the mycoplasmas
firmicutes - lactobacillales, non-sporulating staphylococcus and sporulating bacillus and clostridiales
name some specific actinobacteria? how many taxonomic familes are there?
corynebacterium and arthobacter
theres about 30 taxonomic families and they range from very simple to very complex
some specific examples are: C. diptheriae (diphtheria), C. glutamicum (MSG)
what shape is myobacterium and what are some specific names of bacteria under this category?
they’re rod shaped and some specific names are M. tuberculosis, M. leprae
what is the acid fast test?
it is used to see if a tissue sample is infected with TB
what does filamentous actinobacteria make?
it is commercially the most important bacteria as it makes 70% of antibiotics
what are specific names of filamentous actinobacteria and where are they found?
they inhabit soil and some names are streptomyces and norcardia
what is the biggest threat to bacteria?
getting infected by viruses
what are commercially the most important bacteria?
filamentous actinobacteria
they produce 70% of antibiotics and the cancer drug fk506
how do filamentous bacteria grow/ produce new ones?
they branch at the tip to grow, not by dividing
what are the key genera of tenericutes?
mycoplasma and spiroplasma
what are the key characteristics of tenericutes?
they lack cell walls
they’re some of the smallest organisms capable of autonomous growth
theyre parasites that can inhabit animal and plant hosts
key components of peptoglycan are missing
theyre pleomorphic
what does it mean if cells are pleomorphic?
it means that cells can either be cocci or filaments of various lengths
how can you see how different species of microorganisms are related?
by phylogeny you can find out what they’ve evolved from
what does it mean if an organism is a parasite?
it means that they can only grow within other organisms
what are the key genera of firmicutes?
lactobacillus and streptococcus
what are the key characteristics of firmicutes?
theyre fermentitive bacteria that produce lactic acid
where are lactobacillus found?
theyre common in dairy products, sauerkraut
what pH can lactobacillus grow in?
they’re resistant to acidic conditions so they can grow in pHs as low as 4
what bacteria produce yoguhrt?
a mixed culture of streptococcus salivarius subsp. thermophilus and lactobaillus debrucki subsp. bulgarus
fermentation of lactose produces lactic acid
what are some key genera of streptococcus?
lactococcus
enterococcus
streptococcus
what shape are streptococcus?
theyre coccus shaped
how do streptococcus grow?
they grow in chains
what do streptococcus play important roles in?
in the production of buttermilk, sileage and other products
what do enterococcus cause?
urinary tract infections, bacteremia, endocarditis, diverticulitis and meningitis
what do streptococcus cause?
plaque and pathogens
where are Nonsporulating Bacillales and Clostridiales usually found?
on the skin
what does S. aureus cause?
MRSA (methycilin resistant S aureus
what are sporulating bacullales and clostridales distinguished on the basis of?
on the basis of cell morphology and on the shape and cellular position of endospore
where are sporulating bacillus and clostridium found?
in soil and the endospores are advantageous for soil microorganisms
what types of bacteria can form endospores, have low GCs and are gram positive?
bacillus, clostridium and sporsarcina
what are bacillus, clostridum and sporosarcina distinguished by?
by their cell morphology, relationship to O2 and energy metabolism
where are endospore forming bacteria found?
in soil, the spores are very resistant to everything
what is the gram positive equivalent of E. coli?
B. subtilis
what causes the spore to be at one end of the cell?
cellular asymmetry
how does clostridium produce ATP?
by substrate level phosphorylation
some colostridum species perform stickland reactions, what are these?
theyre metabolism of pair of amino acids
where are clostridium mostly found?
in anerobic pockets in the soil, they also live in mammalian intestinal tracts
can some species of clostridium be pathogenic?
yes
what diseases can clostridium cause?
botulinum, tetanus and gangrene
C. botulinum, C. tetani, C. perfringens
what is the life cycle of bacillus anthracis starting from the multiplication of bacilli?
multiplication of bacilli in mammal > sporulation in mammal> spores form in the soil > germination in the mammal again
what is the system to evade the immune system for bacillus anthacis?
they can make toxins and have the capsule and S layer,then the organism can sporulate and spread
what are the forms of anthrax? and what are the prognosis of these different forms?
cutaneous- insect bite, cut ect (this has a fair prognosis)
gastorintestinal - eating contaminates meat (intermediate prognosis)
inhalation (pulmonary) - inhaling spores (poor prognosis)
all these types can progress into fatal, systemic anthrax though
what is the surface structure of vegetative B. anthracis cells?
all bacteria have a cell membrane and peptoglycan layer
very few have both a capsule and an S layer
what is a capsule in bacteria?
they’re linear polymers of γ-D-glutamic acid
what is the S-layer?
its a proteinaceous paracrystaline sheath
what are AB toxins?
they’re toxins with intracellular targets that have 2 functionally distinct regions
what are the A and B parts of AB toxins?
A- this has enzymatic activity
B- this is responsible for host cell bindign or entry of A unit to cell
what are the 2 ways that AB toxins operate?
- single polypeptide that is proteolytically cleaved at a later stage
- separate polypeptides that subsequently assemble
why are there 2 different subunits of AB toxins?
if there are 2 subunits then one can form a subunit for the other
what are the 2 toxins produced by anthrax?
lethal factor and edema factor
what happens when anthrax releases a primary antigen?
it attaches to the cell then a 7 primary antigen unit pore forms
this imports H+ ions and the pH drops which degrades the signalling compounds inside the cell
what does cAMP do in the cell when its infected with anthrax?
it acts as a signalling molecule which is an alarm signal for the cell, which screws up the signalling in the cell, causing it to die
how much of the biomass on earth is made up of microbes?
~50%
what is the isolation in pure culture important for?
- detailed studies in controlled environments
- biotechnology applications (industrial or environmental microbiology)
why would you separate a microbe from its enviroment?
to see if its an appropriate organism to break down the environment
why is it difficult to grow pure cultures in isolation?
because they live in communities in the environment with lots of small colonies of microorganisms living in this environment
what are biofilms?
they’re assemblages of bacterial cells adhered to a surface and enclosed in an adhesive matrix exerted by the cells
why do bacteria form biofilms? [several reasons]
- self-defence
- allows bacterial cells to live in close association with one another
- example- pseudomonas aeruginosa in CF lung
- c-di-GMP microbial hormone that controls biofilm formation
what are the characteristics of biofilms?
- its usually a mixture of polysaccharides
- they trap nutrients for microbial growth and help prevent detachment of cells flowing systems
- the resist physical forces that sweep away unattached cells, phagocytosis by immune cells and penetration of toxins
what are biofilms a problem for?
industry and health
treating infections
plaque
endotitus
people with cystic fibrosis
what are the 2 ways of microbial isolation from the environment?
direct isolation
enrichment culture
what is direct isolation?
- its when you extract microbes from the enviroment, eluent to release it from the solid matrix
- dilute and plate out
- used for enumeration
basically its when you take a sample and shake it up, pull all the bacteria from it and then plate and count them
how is an enrichment culture formed?
-extract microbes and use eluent to release the cells from the solid matrix
- enrich
- dilute and plate out
- useful for isolation and risk assessment
what is a direct culture?
its when you isolate the microorganism from the enviroment, study its properties in lab cultures
what is isolation culture important for?
- detailed studies in controlled enviroments
- biotechnology applications
what are the medium and incubation conditions selected and de-selected for in direct cultures?
selected for desired organism
de-selected for undesired organisms
what would you add to the culture if you wanted to only grow antibiotic resistant bacteria?
antibiotics
what conditions do you want to mimic when growing a direct culture?
the conditions that the organism is used to growing in
what are the two states of mediums that diect cultures can be grown on?
on a plate or in a liquid culture
what are a few ways that pure cultures can be obtained?
streak plate
agar shake
liquid dilution (MPN- later)
how is an enrichment culture made?
- extract microbes from sample
- enrich
- dilute and plate out
- useful for isolation and risk assessment
what is azotobacter?
its an N-fixer
how are aerobic cultures grown?
on plates
how are anaerobic bacteria cultures grown?
agar shake-tube method - its a dilution of mixed cultures in tues of molten agar
anaerobic jar
what are the different methods of microbial enumeration?
- direct counting
- variable cell counts
- most probable numbers (MPN)
what is direct counting?
its when you count all the cells, alive and dead, you cant distinguish between live and dead cells without a special stain
what are the disadvantages of direct counting?
cant tell the difference between live and dead cells
small cells can be overlooked
precision is difficult to achieve
phase-contrast microscope is needed if a stain isn’t used
low density cell suspensions (<10^8 cells/ml) are hard to count
motile cells need to be immobilised
debris in the sample can be mistaken for cells
what are variable cell counts?
theyre the measurement of the living, reproducing population of cells in the sample
what are the 2 main ways to perform plate counts?
- spread-plate method
- pour-plate method
what do you need to do to the cell sample to obtain the appropriate colony number?
the sample needs to be diluted
what is most probable numbers (MPN) cell count ?
its a serial dilution of inoculum on liquid medium until the final tube shows no growth
estimation of microbial numbers for routine sampling
how do you check for purity in MPN?
- microscopy
- colony characteristics on plate
- test for growth in other media
- check for contamination (failure to grow in the media in which it should be growing well)
what are the two methods organisms can use to balance growth and death rates?
oligotroph - microbes that grow continuously, but at low levels of activity
copiotroph- microbes that are primarily in a resting phase with brief periods of activity when there are nutrients present
what are the nutrient uptake enzymes’ specificity and affinity levels for copiotrophs and oligotrophs?
copiotrophs - nutrient uptake enzymes with high specificity but low affinity
oligotrophs - nutrient uptake enzymes with low specificity but high affinity
what are viable but nonculturable (VBNC) bacteria?
these are bacteria in a state of very low metabolic activity that cant divide and cant grow on standard growth media
they have reduced nutrient transport, respiration and synthesis of macromolecules
what do VBNC arise as a response to?
- nutrients
- temperature
- osmotic
- oxygen
- light
how can VBNC beocme culturable?
alive and have the ability to become culturable once resuscitated
what is an example of a viable but non-culturable bacteria?
vibrio cholerae which can lay dormant in water and then infect people with cholera
what is antibiotic hunting?
its looking for defined target or general activity through novel compounds or novel applications
a well designed screen should hot a novel target
what are some sources for antibiotic hunting?
natural products - fungi, plants, bacteria (especially actinobacteria)
synthetic
semi-synthetic
what are zones of inhibition?
theyre when a filter disc soacked in test compont is put on an agar plate and it forms a lawn of indicator organism where the growth of the organism is inhibited
what are antibiotic susceptibility testing by dilution methods for sensitive organisms?
- determination of minimum inhibitory concentration (MIC)
- increasing conc of antibiotic prepared in culture medium
- inoculated with test organism; growth occurs with concentration below MIC
what can genome mining find?
new antibiotics from genome sequences
what happens when mining with microorganisms?
- Sulphides also form insoluble minerals with metals
Economically feasible to mine low-grade ores only if the metal can be concentrated - The removal of valuable metals, such as copper, from sulfide ores by microbial activities
In microbial leaching, low-grade ore is dumped in a large pile (the leach dump), and sulfuric acid is added - The liquid emerging from the bottom of the pile is enriched in dissolved metals and is transported to a precipitation plant
- Bacterial oxidation of Fe2+ is critical in microbial leaching as Fe3+ itself can oxidize metals in the ores
what types of bacteria are involved in the bioremediation of uranium-contaminated environments?
geobactur
shewanella
what can organic pollutants be completely broken down into by microbes?
CO2
what types of microbes have been used to clean up oil spills?
prokaryotes
what microbes can oxidise petroleum products aerobically?
diverse bacteria, fungi and some cyanobacteria and green algae
when is oil-oxidising activity best? [in terms of temperature]
its best if the temperature and inorganic nutrient concentrations are optimal
what do hydrocarbon-degrading bacteria attach to, to disperse the slick?
they attach to oil droplets and decompose the oil and disperse the slick
what are xenobiotic compounds?
theyre synthetic chemicals that arent naturally occuring
what are some examples of xenobiotic compounds?
pesticides
polychlorinated biphenyls
munitions
dyes
chlorinated solvents
many degrade extremely slowly
what are some characteristics of xenobiotic compunds?
they’re common components of toxic waste
they include herbicides, insecticides and fungicides
what are some of varieties of compounds that can be classed as xenobiotic compounds?
some can be used as carbon source by microorganisms
some can be used as electron donors
what are polyhydroxyalkanoates (PHAs)?
they’re linear polyesters used as storage compounds by bacteria
they are biodegradable and are used in the production of bioplastics
what does the biodegradation of PHA under aerobic conditions result in?
it results in CO2 and water
what does the biodegradation of PHA under anaerobic conditions result in?
it results in CO2 and CH4
