Biofilms Midterm

3 kingdoms

Bacteria

Archaea

Eukaryota

total number of bacterial cells on earth

10^30

upper temp limit of life

120 C

deepest known living bacteria

5+ Km

eukaryotic microbes

viruses, protozoans, fungi, algae, prions

bacterial cell size

1 micron

eukaryotic cell size

several mm

archaea are more closely related to

eukarya

Universal ancestor to all kingdoms

LUCA

archaea

extremophiles

archaea tRNA

different from bacteria and eukaryotes

archaea ribosomes

similar to eukaryotes, different from bacteria

archaea cell membranes

glycerol

What kingdom has the smallest genome

archaea (550 genes)

what kingdom has the largest genome

eukarya (humans have 23,000 genes)

turgor pressure

bacterial cells are under high internal pressure

how do bacteria reproduce

binary fission

lag phase

cells adapting to environment, no growth

log phase

most active growth phase, lasts short period of time

generation time

time it takes cells to double, how long until cells divide

stationary phase

unbalanced growth, chemical composition changes

death phase

decrease numbers of viable cells with time

most antibiotics target what phase

log phase

inactivity of bacteria

shut down metabolism when stressed

intermittent growth characterizes

most bacteria in natural ecosystems

resistant stages of bacterial cell growth

spores, GASP, VBNC, persister cells

GASP

growth advantage in stationary phase

VBNC

viable but non-culturable

when do spores form

in dry environments

where do spores form

inside of cell, hard coating on outside

spores are resistant to

heat, radiation, chemicals, acids, drying

persister cells

dormant (non-active) but not spores, do not have hard coating

where do persister cells occur

recurrent infections, why infections can’t be completely killed

how do molecules get in and out of cells

diffusion (passive), active transport (porins)

surface area to volume ratio

rate of nutrient transfer is better when cells are smaller

why are bacteria so adaptable

genetic variability: high mutation rates, recombination

genetic variability

needed for individuals in the population to survive in changing environments

high mutation rates

random changes in DNA can result in beneficial changes to cell

recombination

process that leads to new gene combinations on a chromosome

house keeping genes

genes required for normal cell functioning

ancillary phenotypic genes

not needed by cells under all conditions (resistance genes)

what type of genes are usually on plasmid

ancillary genes

conjugation

transfer of genetic material that is facilitated by pili, requires direct cell to cell contact

transformation

competent cell absorbs foreign genetic material from the environment

transduction

gene transfer involving a viral vector

brownian motion

random movement from bacteria bumping into each other

directed motion

movement using flagella

primary producers

fix carbon and nitrogen

decomposers

breakdown organic material, cycle carbon, nitrogen, and sulfur

commensals

assist in growth and efficiency of plants and animals

pathogens

harm host organisms

free-living cells

planktonic growth

attached cells

biofilm growth

conditioning film

molecules that settle on a surface and make it stickier for bacterial cells

EPS

extracellular polymeric substances

state 1 of biofilm

attachment

state 2 of biofilm

growth, EPS

state 3 of biofilm

detachment

does gene expression change in bacteria upon biofilm formation

yes

changes in gene expression in biofilms

* loss of motility (flagella)
* polymer production/secretion
* stationary phase
* activation of stress-induced pathways
* unknown genes expressed

advantages of biofilm state

* attachment (secure)
* protection (dehydration, radiation, antibiotics, etc)
* localization of enzymes
* better cell-cell communication/gene exchange

what state of cell growth is most adaptable

biofilm

antibiotic resistance in biofilms

antimicrobial resistance mechanisms of different cells can work together to strengthen resistance

biofilm cell phenotypes

1. actively growing
2. variability (mutation, gene exchange)
3. autolytic (suicide)
4. persister
5. dispersal (VBNC)

are biofilms good or bad for industry, health, environment

mostly bad, can be beneficial

positive effects of biofilms

commensal bacteria in skin and gut

examples of negative effects of biofilms

biofouling, antibiotic resistant infections

exuding surfaces

permeable, biological (soft tissue surfaces)

non-exuding surfaces

non-permeable (metal, plastic)

steps to inhibit biofilm formation

* prevention of adhesion
* disruption of attached cells
* disruption of formed biofilm

\#1 emergent property of biofilms

EPS matrix

physical states of EPS

* capsules- surrounding cells
* slime - loose matrix
* gel- tight matrix
* dissolved- suspension

physical properties of EPS

* highly hydrated (97-99% water)
* sorptive - binds stuff
* protective
* diffusion slowing- localization of stuff

what makes EPS sorptive

functional groups

why do cells use carbs in EPS

carry information, bond several possible ways

dextran

linear homopolymer of glucose monomers

alginate

linear heteropolymer of mannuronic and guluronic acid

uronic acids

negative charge, bind cations well

secretion of eps

monomers transported by carrier proteins through porins

proteins for EPS

* extracellular enzymes
* structural proteins (beta-amyloid)
* lectins - carbo-binding proteins
* glycoproteins- carb with sugars covalently linked to proteins
* proteoglycans

localization of extracellular enzymes

EPS keeps enzymes close to cell so cell can benefit from hydrolysis products

why are extracellular enzymes necessary

bacteria can only take up small molecules, large molecules must be hydrolysed

desiccated biofilms

biofilms can dry up and revive when water is introduced

EPS glass

high-viscosity liquid that protects proteins from dehydration, allows microbial community to “sleep” when desiccated

nucleic acids in EPS

* structural
* lysis products
* plasmids

continuous exposure to metals

selects for bacteria/EPS that facilitates metal removal

agonistic relationship

positive bacteria-bacteria relationship

antagonistic relationship

negative bacteria-bacteria relationship

commensal relationship

neutral bacteria-host relationship

symbiotic relationship

bacteria-host relationship in which each benefits and requires the other

pathogenic relationship

bacteria-host relationship in which one causes harm to the other

microspatial clustering of bacteria in natural biofilms

groups of the same bacteria will form within biofilm

signal

cue, highly specific

diffusion sensor

probes envirnment

chemical signaling density dependence

cells must be close together to detect signals that diffuse

step 1 of quorum sensing

sensing and binding of signal

step 2 of quorum sensing

gene activation/repression

step 3 of quorum sensing

protein expression changes

step 4 of quorum sensing

physiological changes

step 5 of quorum sensing

coordination of activities