Microbial Growth + Biofilms Flashcards
Which one of the statements is true?
1) Unlike all living things, microorganisms do not need sources of carbon and energy to grow.
2) Due to the PLASTICITY OF MICROBIAL GENOMES, bacteria have evolved ingenious strategies to find, acquire and metabolize wide source of food
3) Controlling bacterial cell growth is impossible; understanding how bacteria use food to increase cell mass and cell number can do only so much.
2 is true!
Like all living things, microorganisms DO need sources of carbon and energy to grow.
Understanding how bacteria use food to increase cell mass and cell number ENABLES US to control bacterial growth! It can even allow us to MANIPULATE them to make useful products!
Fill in the blanks:
Essential nutrients are those that MUST be supplied from the _____________.
______ nutrients are needed in large amounts (major elements in cell macromolecules and cations for protein function).
______ nutrients are needed in small amounts (trace elements needed 2 enzyme function).
Environment
Macro; Micro
(T/F) Majority, but not all, of Earth’s life-forms are carbon-based.
False. ALL of Earth’s life forms are carbon based!
Which organisms fix CO2 and assemble into organic molecules, and which ones use performed organic molecules to build biomass?
A) Photoautotrophs
B) Chemoorganoheterotrophs
C) Chemolithoautotrophs
D) Photoheterotrophs
All autotrophs fix CO2 and assemble into organic molecules and all heterotrophs use performed organic molecules (to make more).
Membranes separate insides and outside of a cell, what are the three ways SELECTIVE PERMEABILITY is achieved?
1) Substrate-specific carrier proteins (PERMEASES)
2) Dedicated NUTRIENT-BINDING PROTEINS that patrol the periplasmic space
3) Membrane-spanning PROTEIN CHANNELS/PORES (transporters)
What are three sources of energy that can cause a molecule to go against its concentration gradient (active transport)?
ATP
Proton motive force (PMF)
PEP (high energy molecules in bacteria)
What is the largest family of energy-driven transport systems?
ATP-binding cassette superfamily (ABC transporters)!
(T/F) ABC transporters are found in all three domains of life, and over 200+ different systems identified in eukaryotes for organic and inorganic compounds.
False! ABC transporters are found in all three domains of life, but over 200+ different systems identified in PROKARYOTES for organic and inorganic compounds.
Match the following terms regarding ABC transporters:
1) Gram-negatives
2) Gram-positives and Archaea
3) Uptake ABC transporters
4) Efflux ABC transporters
A) used as multi drug efflux pumps, throw drugs OUT of the cell
B) employ PERIPLASMIC BINDING PROTEINS
C) critical for transporting nutrients INTO the cell
D) employ substrate-binding proteins on EXTERNAL SURFACE OF CYTOPLASMIC MEMBRANE
Gram-negatives employ PERIPLASMIC BINDING PROTEINS
Gram-positives and Archaea employ substrate-binding proteins on EXTERNAL SURFACE OF CYTOPLASMIC MEMBRANE
Uptake ABC transporters critical for transporting nutrients INTO the cell
Efflux ABC transporters, used as multi drug efflux pumps, throw drugs OUT of the cell
Match the following steps of an uptake ABC transporter transporting a solute inside a gram negative cell:
1) Step 1
2) Step 2
3) Step 3
A) When the solute binds to the membrane transporter, conformational change activates ATPase.
B) After ATP hydrolysis, the dimer opens and releases the solute to the cytoplasm.
C) Solute binds to its cognate periplasmic binding protein, and the complex then binds to the membrane transporter
Step 1: Solute binds to its cognate periplasmic binding protein, and the complex then binds to the membrane transporter
Step 2: When the solute binds to the membrane transporter, conformational change activates ATPase.
Step 3: After ATP hydrolysis, the dimer opens and releases the solute to the cytoplasm.
(T/F) Microbes exist in complex, multispecies communities in nature and they can be grown together for detailed studies.
False!Microbes exist in complex, multispecies communities in nature but they have to be grown SEPARATELY in PURE CULTURE!
(T/F) After almost 140 years of trying, we have succeeded in culturing less than 1% of the microorganisms around us. The vast majority has yet to be tamed.
True!
Match the following culture media bacteria are grown in and what it is used for:
1) Liquid/broth
2) Solid (gelled with agar)
A) Useful for trying to SEPARATE MIXED CULTURES from clinical specimens or natural environments
B) Useful for studying the growth characteristics of a PURE CULTURE
1) Liquid/broth: Useful for studying the growth characteristics of a PURE CULTURE
2) Solid: Useful for trying to SEPARATE MIXED CULTURES from clinical specimens or natural environments
What are obligate intracellular bacteria? Give an example.
Bacteria that are unculturable! They absolutely require an eukaryotic host to survive and replicate.
Epidemic typhus fever bacteria (Rickettsia Prowazekii) can only grow within cytoplasm of eukaryotic cells and nowhere else.
*some can be cultured within host cell
Match the following terms regarding the growth cycle to their definition:
1) Growth
2) Binary fission
3) Septum
4) Generation time
A) Partition between dividing cells, pinches off between two daughter cells
B) Cell division following enlargement of a cell to twice its minimum size
C) Time required for microbial cells to DOUBLE in numbers; depends on NUTRITIONAL, GENETIC factors and TEMPERATURE
D) Increase in the number of cells
1) Growth: increase in the number of cells
2) Binary fission: cell division following enlargement of a cell to twice its minimum size
3) Septum: partition between dividing cells, pinches off between two daughter cells
4) Generation time: time required for microbial cells to DOUBLE in numbers; depends on NUTRITIONAL, GENETIC factors and TEMPERATURE
(T/F) During cell division, each daughter cell receives a chromosome and sufficient copies of all other cell constituents to exist as an independent cell.
True!
Briefly describe how cell division by septation occurs, also the role of FtsZ and Divisome.
After DNA synthesis terminates, a septum grows inward from the sides of the cell.
FtsZ circles around the septum and directs its growth (SEPTUM FORMATION). When FtsZ’s ring contracts, the cytoplasm of the two daughter cells separate.
Cell wall forms and the cell finally separates as individual cells.
Divisome is the protein complex that manages septation, which Ftsz is a part of.
What kind of cell division leads to equal products? How common is this?
BINARY FISSION; most bacteria
What kinds of cell division lead to unequal products?
Budding division from UNEQUAL CELL GROWTH or ASYMMETRIC GROWTH.
1) Simple budding - one side of the cell is new material, that one daughter cell is composed of.
2) Budding from hyphae
3) Cell division of stalked organism
4) Polar growth without differentiation of cell size
What are stalks, hyphae and appendages that budding bacteria form?
Cytoplasmic extensions
What is a closed culture? What is it also known as?
Culture with LIMITED NUTRIENTS. Also known as BATCH culture.
Match the phases of a bacterial growth curve of a closed culture:
1) Phase 1
2) Phase 2
3) Phase 3
4) Phase 4
A) Death/decline phase
B) Lag phase
C) Log phase
D) Stationary phase
Phase 1 - Lag phase
Phase 2 - Log phase
Phase 3 - Stationary phase
Phase 4 - Death/decline phase
Match the phases of a bacterial growth curve of a closed culture to their definition:
1) Lag phase
2) Log phase
3) Stationary phase
4) Death/decline phase
A) Exponential decrease in number of bacterial cells
B) No increase in number of living bacterial cells
C) Exponential increase in number of living bacterial cells
D) Plateau in number of living bacterial cells; RATE OF CELL DIVISION = RATE OF CELL DEATH
1) Lag phase: No increase in number of living bacterial cells
2) Log phase: Exponential increase in number of living bacterial cells
3) Stationary phase: Plateau in number of living bacterial cells; RATE OF CELL DIVISION = RATE OF CELL DEATH
4) Death/decline phase: Exponential decrease in number of bacterial cells
Why are log measurements used in bacterial growth curves?
Number of cells increase rapidly, and they double at the same amount of time in their best growth phase (log phase); log scale helps to visualize the complete curve.
When plotted on an ARITHMETIC SCALE (equal spacing for x and y values), the growth rate resembles a ________.
When plotted on a SEMILOGARITHMIC SCALE, (y-value are logarithmic, x-values are arithmetic), the growth rate appears _______.
Curve
Linear
What is a continuous culture?
What does the population in a continuous culture achieve? What does this allow study of?
Continuous culture - bacteria grown in a culture where the nutrients are not limited!
The bacterial population achieves a STEADY STATE. This allows DETAILED study of BACTERIAL PHYSIOLOGY.
Fill in the blank:
The _______ ensures logarithmic growth by constantly adding and removing equal amounts of culture medium in a continuous culture.
CHEMOSTAT
What human tract is engineered much like a chemostat?
The GASTROINTESTINAL tract
Chemostat ensures log growth of bacteria by adding and removing equal amounts of culture medium!
(T/F) Continuous culture provides with denser bacteria, which is good for things like insulin!
True!
What are biofilms?
Specialized, surface-attached communities formed by bacteria.
What are four main characteristics of biofilms?
1) Biofilms can be constructed by ONE OR MORE SPECIES, concern all matter of life
2) Biofilms can form on a range of ORGANIC or INORGANIC SURFACES (medical devices, blockage of petrol pipes, biofilms on boats reduce glide)
3) Biofilms are HARDY (difficult to dislodge)
4) Biofilms PROTECT BACTERIA (prevent antibiotics from penetrating, prevent protists from grazing)
(T/F) Detergents and sterilizing agents can effectively kill biofilms as it can kill living bacterial cells.
False! Detergent and sterilizing agents are not as effective on biofilms as they are on living bacterial cells.
What kind of conditions do biofilms form in? What happens in opposing conditions?
They form when NUTRIENTS ARE PLENTIFUL.
When nutrients become scarce, individuals detach from the community to forage for new sources of nutrients!
(T/F) Biofilms in nature take many forms and functions for different species. The formation of biofilms can be cued by the same env signal for different species!
False! Biofilms in nature do take many forms and functions for different species. However, the formation of biofilms can be cued by DIFFERENT ENV SIGNALS in different species.
What is quorum sensing?
A way of bacteria to communicate with one another (when in large volumes) using CHEMICAL SIGNALS, and in some cases to FORM BIOFILMS.
What are the three things biofilm development involves?
1) The ADHERENECE of cells to a substrate
2) The formation of MICROCOLONIES
3) Ultimately, the formation of COMPLEX CHANNELED COMMUNITIES that generate new planktonic cells
What are the five stages of biofilm life cycle?
1) Attachment to monolayer by flagella
2) Formation of microcolonies (gene expression changes here and the flagellas are lost)
3) EXOPOLYSACCHARIDE (EPS) production
4) Mature biofilms
5) Dissolution and dispersal (enzymes are secreted that digest the EPS layer and cells with flagella are dispersed)
Which one of the following sentences in false?
1) Water can not freely move through the biofilm structure.
2) Biofilms make bacterial colonies 10-1000x more resistant to antimicrobials.
3) Biofilms cost lots of money in the medical field to get new equipments.
1 is false! Water CAN move freely through the biofilm structure.
Briefly describe how a biofilm forms in the sea.
1) Bacterial cells settle onto hard surface.
2) Cells proliferate and secrete slime, forming a biofilm.
3) Some cells detach.
4) Protists graze on bacteria.
5) If enough biofilm forms, large organisms can attach to it.
Bacteria growing in biofilms exhibit a type of CELL DIFFERENTIATION initiated by physiological conditions that develop in different layers of the biofilm.
If cells have some pili/flagella, they are most likely in ________ growth phase.
If cells are in a mesh of pili and flagella, they are most likely in _______ or ______ phase.
Exponential
low growth; decline (no growth)
Which one of the statements regarding biofilm and medicine false?
1) Mucosa are covered in biofilms, this can be good or bad depending on bacteria.
2) Luckily, bacterial infections do not involve the formation of a biofilm at some point.
3) 60-70% of hospital derived infections are caused by biofilms of medical devices.
2! UP TO 80% of bacterial infections involve the formation of a biofilm at some point.
Biofilms associated with chronic infections and are difficult to treat.
How can biofilms limit penetration and increase biofilm resistance?
1) Electrostatic interactions
2) Hydrophobic interactions
3) Size exclusion
4) Degradation of biocides
Biofilms associated with chronic infections and are difficult to treat.
How can biofilms, besides limiting penetration, increase biofilm resistance?
1) Biofilm phenotype - changes in gene and protein expression
2) Persister cells - exhibit multidrug tolerance WITHOUT genetic change
3) Slow growth - limits cell’s uptake of biocides
4) Adapted cells - develop a greater tolerance
(T/F) Even with homogenous biofilm, certain cells express different genes (CELL DIFFERENTIATION) and PERFORM DIFFERENT FUNCTIONS within the community.
True!
Changes in genetic expression can change planktonic state to a sessile state; some cells can have greater motility whilst others sporulate.
(T/F) Composition of biofilms depend on the nature of materials on which biofilms are formed (biotic/abiotic) but not the bacterial species.
False! Composition of biofilms depend on the nature of materials on which biofilms are formed (biotic/abiotic) and also the bacterial species.
*what they adhere to, they can change what biofilm they are making
What are molecular constitution of biofilms largely constituted of?
1) Exopolyosides (EPS) or Extracellular Polymeric Substances
2) Proteins (type IV pili)
3) eDNA (extracellular DNA)
Briefly describe the neglected role of DNA in biofilms.
Under the control of quorum sensing, certain bacteria release DNA outside of their cell. Other cells can release as they die.
DNA is (-) and if it accumulates around bacteria, it protects them from antimicrobials which are generally (+).
DNA is sticky; helps biofilm structure + coherence. It can also make it difficult for immune cells or competitors to penetrate the structure.
This could favour the EXCHANGE OF GENETIC MATERIAL within the biofilm communities.
It can also serve as a SOURCE OF NUTRIENTS in oligotrophic conditions (low lvl nutrients)
(T/F) What composes the biofilms can vary even within a single bacterial species.
True!
What is critical in the development and maintenance of a biofilm?
Quorum sensing
What is the major intracellular signalling for quorum sensing in gram (-) bacteria?
Acylated homoserine lactones (AHLs)
(T/F) AHLs are produced only when bacteria want to form biofilms.
False. AHLs are formed all the time by bacteria, but when there is a lot forming due to a lot of bacteria, biofilm forms!
(T/F) Both INTRAspecies and INTERspecies signalling occur in biofilms.
True!
Acummlation of _____, an autoinducer indicates population of P.aeruginosa (a gram negative bacteria) is growing, which triggers genes for extraceullar polysaccharide and ________ synthesis.
acyl homserine lactones (AHLs)
C-di-GMP (cyclic di-guanosine monophosphate)
What is the role of C-di-GMP in biofilm formation in P. aeruginose?
When C-di-GMP synthesis is trigged by the accumulation of autoinducers, it initiates physiological effects:
1) Binds to proteins to REDUCE FLAGELLAR ACTIVITY
2) REGULATE attachement proteins
3) Mediate BIOSYNTHESIS of extracellular matrix polysaccharides
(T/F) When bacterial cells are quorum sensing, they are in a reversible phase of biofilm production but when bacterial cells express c-di-GMP, they are in the irreversible phases of biofilm production.
True!
V.cholerae, an aquatic bacteria, forms biofilms during the ______ and _____ phases of its life cycle.
Aquatic; intestinal
(T/F) Both toxigenic and non-toxigenic V.cholerae strains live in the aquatic environment year-round, either in a planktonic state or in a biofilm.
True!
What do toxic V.cholerae strains colonize in humans when ingested (typically through contaminated water/food)?
What do they do there?
SMALL INTESTINE
They multiply and produce CHOLERA TOXIN, causing severe illness to the host.
When V.cholera is shed in the stool, what are its two possible pathways?
1) Re-enter the aquatic environment
2) Infect a new host
(T/F) V. cholerae outbreaks occur all the time.
False, they are seasonal and correlate with changes in environmental conditions.
What is the major environmental factor affecting seasonal outbreaks of V.cholerae?
The occurrence of PLANKTON BLOOMS.
How is quorum sensing different in V.cholerae than in P. aeruginosa?
Quorum sensing of V.cholerae acts OPPOSITE to QS of P.aeruginosa.
When quorum sensing molecules accumulate in P.aeruginosa, C-di-GMP is synthesized which triggers biofilm formation that deactivate flagellar genes.
When quorum sensing molecules accumulate in V.cholerae, C-di-GMP is inhibited which inhibits biofilm formation, but activate flagellar and virulence genes.
Biofilm formation in V.cholerae is triggered by low densities (increases C-di-GMP), repressed by high cell densities (decreases C-di-GMP)!
How can we use biofilm formation knowledge to our advantage?
1) Design materials that will be RESISTANT to biofilm formation
2) Coat materials with molecules that PREVENT biofilm formation
3) Inhibit the dissemination of quorum sensing signals stimulating biofilm formation (QUORUM QUENCHING)
4) INHIBIT RECEPTOR of quorum sensing molecules (another form of quorum quenching)
What are microbial mats?
Very thick biofilms
Microbial mats are found in ______ environments, and are built by _______ and _______ bacteria.
Extreme
Phototrophic; chemolithotrophic
What do phototrophic mats contain? What do chemolithotropic mats contain?
Phototrophic –> filamentous cyanobacteria (complete ecosystems)
Chemolithotropic -> filamentous sulfur-oxidizing bacteria
What causes unique niches at different depth within the microbial mats?
Steep concentration gradient created by the combination of microbial metabolism and nutrient transport.
