Biofilms and Bioluminescence Lecture Notes

Flashcards about biofilms, quorum sensing and bioluminescence.

Why are surfaces important microbial habitats?

Nutrients adsorb to surfaces, allowing microbial cells to attach.

What are biofilms?

Assemblages of bacterial cells adhered to a surface and enclosed in an adhesive matrix excreted by the cells. .

What do biofilms do?

Biofilms trap nutrients for microbial growth and help prevent detachment of cells in flowing systems.

What is the matrix and what does it consists of?

The matrix is a complex mixture of polysaccharides and creates a sticky surface

What are the features that distinguish biofilm populations from their planktonic counterparts?

The association with a surface, high population densities (on the order of 10^{10} cells per ml of hydrated biofilm), an extracellular polymer (EPS) slime matrix, and a wide range of physical, metabolic and chemical heterogeneities.

What are biofilms responsible for?

Biofilms, along with flocs and microbial mats, drive most microbial conversions in natural environments.

Where can biofilms be found?

Biofilms are ubiquitous, covering rocks, plants, sediment grains, and sediment surfaces in seawater and freshwater.

How does biofilm formation begin?

It starts with a cell attaching to a surface, followed by the expression of biofilm

What do biofilm-specific genes encode?

encode proteins that synthesize intercellular signaling molecules and initiate matrix formation.

Why are biofilms important?

,They play a crucial role in microbial communities, enabling surface colonization and biochemical interactions.

What are flocs?

Aggregates of cells and extracellular matrix that are like floating surfaces

What are microbial mats?

are like layers of metabolisms based on reduced compounds on bottom and oxidized on top

What is the first step of biofilm formation?

Attachment: Individual bacterial cells adhere to a surface using pili, flagella, or adhesive proteins.

What happens after attachment in biofilm formation?

Microcolony Formation: Attached cells begin dividing and forming small clusters which causes intracellular communication growth and polysaccharide forming.

What role does the extracellular matrix play in biofilm development?

The matrix binds cells together, providing structural support and protection.

How does a biofilm mature?

The biofilm develops into a structured, three-dimensional community with nutrient channels and cell differentiation.

What is the final step in biofilm formation?

Detachment & Dispersal: Portions of the biofilm break away, spreading bacteria to colonize new surfaces.

Why is biofilm formation important?

It helps microbes survive in diverse environments, including medical, industrial, and natural ecosystems.

What is cyclic di-GMP?

A regulatory molecule that triggers biofilm formation by signaling bacteria to transition from planktonic growth to a semisolid matrix.

Where is cyclic di-GMP found? -

It is widely distributed only in bacteria.

What environmental factors affect cyclic di-GMP? -

Its synthesis and degradation depend on environmental and cellular cues.

How does cyclic di-GMP influence bacterial physiology? -

It can either promote or inhibit physiological events such as differentiation, development, and biofilm-relevant functions

What role does cyclic di-GMP play in biofilm formation? -

It binds proteins that reduce flagellar motor activity, regulate attachment proteins, and mediate extracellular matrix polysaccharide biosynthesis

How is cyclic di-GMP synthesized?

It is synthesized from two GTP molecules via GGDEF domain enzymes.

How is cyclic di-GMP degraded?

Phosphodiesterase domains degrade c-di-GMP into pGpG

Why is cyclic di-GMP important for biofilms?

It enhances adhesion and extracellular matrix production

What effect does cyclic di-GMP have on bacterial motility?

It reduces flagellar motor activity

How does cyclic di-GMP affect transcription factors?

It regulates gene expression related to biofilm formation and bacterial development.

What is the primary reservoir of Pseudomonas aeruginosa?

Soil.

How do Pseudomonas aeruginosa biofilms increase pathogenicity?

They contain polysaccharides that block antibiotic penetration and enhance bacterial survival.

Which condition is worsened by Pseudomonas aeruginosa biofilms in the lungs?

Cystic fibrosis.

What role does quorum sensing play in biofilm formation?

It signals population growth and activates genes for extracellular polysaccharide and c-di-GMP synthesis.

How does elevated c-di-GMP affect Pseudomonas aeruginosa?

It initiates extracellular polysaccharide production and decreases flagellar function, promoting adhesion.

How does DNA contribute to biofilm formation?

DNA released by lysed cells is incorporated into the extracellular polymeric substances (EPS), strengthening biofilms.

What causes 'explosive death' in Pseudomonas aeruginosa cells?

Expression of lysis proteins by inactive prophage in response to stress.

Why does antibiotic treatment sometimes enhance biofilm formation?

It triggers explosive death, releasing DNA that reinforces the biofilm structure.

What is the function of acyl homoserine lactones (AHLs) in Pseudomonas aeruginosa?

They signal population growth and activate biofilm-related genes.

Why is Pseudomonas aeruginosa considered an opportunistic pathogen?

It primarily infects individuals with weakened immune systems.

How is Vibrio cholerae biofilm formation different from Pseudomonas aeruginosa?

Biofilm formation in Vibrio cholerae is triggered at low cell densities and repressed at high cell densities

How do quorum signaling molecules affect Vibrio cholerae biofilm formation?

They accumulate at high densities, repressing biofilm formation genes and activating flagellar genes for dispersal

What role do biofilms play in Vibrio cholerae’s survival?

Biofilms allow Vibrio cholerae to attach to marine surfaces like plankton, crustaceans, and sediments for better access to nutrients and protection

Why does Vibrio cholerae disperse from biofilms?

Dispersal enables transmission to new host cells, increasing infection potential

What is the ecological significance of Vibrio cholerae biofilms?

They help the bacteria survive in aquatic environments by providing structural stability, nutrient access, and protection

What is known about archaeal biofilms?

Research is still developing, but some biofilm events are similar to those in bacteria

Which archaeon is commonly studied for biofilm formation?

Sulfolobus acidocaldarius

What role does the AbfR1 transcription factor play in biofilm formation?

When phosphorylated, AbfR1 activates biofilm formation by increasing EPS and pili synthesis while reducing archaella production

How does AbfR1 function when unphosphorylated?

It activates archaella production while repressing EPS and pili synthesis, reducing biofilm formation

What environmental factors influence AbfR1 activity?

Changes in pH or temperature may regulate phosphorylation states

How do archaea differ from bacteria in quorum sensing?

Archaea produce quorum-sensing-like molecules but do not use c-di-GMP; instead, they produce c-di-AMP, which may regulate biofilm formation

What is one of the most important practical uses of biofilms?

Biological wastewater treatment

How do municipal wastewater plants utilize biofilms?

Activated sludge plants rely on microbial flocs to process wastewater

What emerging technologies are using biofilms?

Bioreactors employ biofilms for biodegradation and bioremediation

Why do bacteria form biofilms for self-defense?

Biofilms resist physical forces that sweep away unattached cells, protect against phagocytosis, and block penetration of toxins like antibiotics

How do biofilms help bacteria remain in a favorable niche?

Biofilms allow bacteria to stay in environments rich in nutrients and moisture, preventing displacement by fluid movement

What advantage does living in close association provide to bacteria in biofilms?

It enables efficient communication, resource sharing, and collective survival strategies

How do biofilms protect bacteria from antibiotics?

The extracellular matrix blocks antibiotic penetration, making treatments less effective

Why do biofilms prevent phagocytosis?

They create a physical barrier that shields bacteria from immune system cells attempting to engulf them

How do bacteria within biofilms communicate?

They use signaling molecules to coordinate activities and adapt to environmental changes

Why is biofilm formation significant for bacterial survival?

It enhances resistance to hostile conditions and improves access to essential resources

What are some examples of types of biofilms?

Biofilms can be found in natural environments like rivers, lakes, and oceans, as well as in man-made settings such as medical devices, dental implants, and wastewater treatment facilities.

What is this image?

A FISH analysis of an activated sludge from waste water treatment. Each color represents different organisms.wastewater

What medical and dental conditions are associated with biofilms?

Biofilms are implicated in periodontal disease, kidney stones, tuberculosis, Legionnaires’ disease, Staphylococcus infections, and others

How do biofilms contribute to medical infections?

They create a protective barrier that shields bacteria from antibiotics and immune responses, making infections harder to treat

What industrial problems can biofilms cause?

Biofilms can slow the flow of liquids through pipelines and accelerate the corrosion of inert surfaces

How do biofilms affect pipelines?

They accumulate inside pipes, reducing flow efficiency and leading to blockages

Why do biofilms accelerate corrosion?

They enhance the deterioration of metals and inert surfaces, affecting infrastructure durability

Are there effective treatments for biofilm-related infections?

Few highly effective antibiofilm agents exist, making treatment and removal difficult

Why is research on biofilms important?

Developing stronger antibiofilm treatments can improve medical and industrial solutions

What is Bioluminescence?

natural phenomenon in which living organisms produce light through biochemical reactions, often used for communication, camouflage, or attracting prey.

What biochemical reaction produces light in Vibrio fischeri?

Luciferase catalyzes the oxidation of FMNH₂, oxygen (O₂), and an aldehyde (RCHO), resulting in light emission

What enzyme is responsible for bioluminescence in Vibrio fischeri?

LuxAB, which encodes luciferase

What are the key products of the luciferase reaction?

Fatty acid (RCOOH), FMN, H₂O, and light

What is the function of LuxC, LuxE, and LuxD?

They generate fatty acid precursors required for aldehyde regeneration in the bioluminescence process

How does LuxG contribute to bioluminescence?

It supplies reducing equivalents by converting NAD⁺ to NADH

Why is bioluminescence important for Vibrio fischeri?

It helps bacteria establish symbiotic relationships with marine hosts and modulates host behavior

Which marine organisms commonly associate with Vibrio fischeri?

Squid and other deep-sea organisms

How does Vibrio fischeri bioluminescence aid squid?

It supports counterillumination, allowing squid to evade predators by matching ambient light

What energy sources are consumed in Vibrio fischeri bioluminescence?

Oxygen, reducing equivalents, and ATP

What is the role of LuxG in bioluminescence?

LuxG facilitates electron transfer by oxidizing NADH to NAD⁺, providing reducing power for FMNH₂ regeneration

How does LuxG contribute to the bioluminescence process?

It ensures FMNH₂ regeneration, which is necessary for sustained luminescence in bacteria like Vibrio fischeri

What is the function of LuxC?

LuxC is involved in aldehyde production and fatty acid metabolism, generating substrate precursors for luciferase reactions

How do LuxC and LuxE work together?

They regulate aldehyde recycling to maintain a steady supply of substrates for bioluminescence

What is the biochemical significance of LuxG?

It maintains redox balance in bioluminescent bacteria and supports the continuous generation of reducing equivalents

How does LuxC influence metabolic pathways?

It links fatty acid metabolism to luminescence by ensuring the availability of aldehyde precursors

How do LuxG and LuxC compare to LuxAB?

While LuxAB catalyzes light production, LuxG supports electron transfer, and LuxC provides necessary metabolic substrates

Why are LuxG and LuxC important for bioluminescence efficiency?

Their coordinated activity ensures the sustained emission of light and metabolic stability

What does LuxAB encode?

LuxAB encodes luciferase, the enzyme responsible for catalyzing the bioluminescent reaction in bacteria like Vibrio fischeri

Which molecules are involved in the LuxAB-catalyzed bioluminescent reaction?

FMNH₂, oxygen (O₂), and an aldehyde (RCHO), which produce light, FMN, a fatty acid, and water

What is the standard reduction potential (E₀') of FMNH₂/FMNH?

The standard reduction potential of FMNH₂/FMNH is -0

Which of the following is a strong electron donor based on reduction potential?

NADH is a strong electron donor with a reduction potential of -0

What is the role of oxygen (O₂) in the LuxAB reaction?

Oxygen (O₂) acts as an electron acceptor in the LuxAB-catalyzed reaction, facilitating the oxidation of FMNH₂ and aldehydes to produce light

Which of the following is a strong electron acceptor based on reduction potential?

O₂/H₂O is a strong electron acceptor with a reduction potential of +0

What is the significance of FMNH₂ in bioluminescence?

FMNH₂ provides reducing power for the light-emitting reaction catalyzed by luciferase, enabling the oxidation process that produces light

What is the reduction potential of NADH/NAD⁺?

The reduction potential of NADH/NAD⁺ is -0

How does LuxAB contribute to bioluminescence?

LuxAB encodes luciferase, which catalyzes the light-emitting reaction in bioluminescent bacteria

What is the role of aldehydes (RCHO) in the LuxAB reaction?

Aldehydes (RCHO) are oxidized to fatty acids (RCOOH) in the LuxAB reaction, contributing to the light-emitting process

Are biofilms and bioluminescence based on density-dependent behavior?

yes

How does cell density affect bioluminescence?

Low cell density results in no bioluminescence, while high cell density activates light production

Why don’t single bacterial cells produce bioluminescence?

Light production requires energy, and it is only beneficial when a large population is present

What is quorum sensing?

A bacterial communication method where cells detect population density and activate bioluminescence genes at a critical threshold