Abiotic vs Biotic
Abiotic = not alive (biofilm forms on objects)
Biotic = alive (biofilm forms on living tissues)
chronic infections
(long-lasting). about 80% of chronic infections in humans involve bacteria living in biofilms.
Pellicle (microbial mats)
-air-liquid interface
-thin layers of bacteria that float at the surface of liquids
Aggregates
-small clumps or clusters of bacterial cells grouped together.
-in suspension
Biofilms
-solid-liquid interface( tooth with saliva)
-larger, more structured communities that attach to surfaces (like teeth, pipes, or catheters).
Studying Biofilms – Microscopy Techniques:
Fluorescence microscopy – uses fluorescent dyes to label specific bacteria or biofilm components, making them glow under a special light.
Scanning electron microscopy (SEM) – gives detailed 3D surface images of biofilms, showing the structure and arrangement of cells.
Confocal scanning laser microscopy (CLSM) – allows 3D imaging of biofilms layer by layer, often used with fluorescent labels.
Studying Biofilms – Community Member Analysis
This focuses on understanding what each bacterial species or gene is doing inside a mixed biofilm community
-Proteomics → studies all the proteins being produced by the bacteria in the biofilm.
-Transcriptional profiling → studies gene expression (mRNA levels).
-Fluorescent reporter genes (like GFP) are genes that make cells glow under specific light, allowing scientists to visually track when and where certain genes are active.
Studying Biofilms – Genetic Analysis:
take bacteria from different enviorments , add transposon mutagenesis which inserts into a gene, it usually disrupts that gene, then Site-specific mutagenesis to test which protien and stuff are needed for biofilm .
Studying Biofilms - Computational
biology
3-D reconstruction of the
bacterial biofilm made by
cholera bacteria
Studying Biofilms – Phenotypic
observing what biofilms look like and how they behave when genes are changed — both on solid plates and in liquid media.
biofilm Structures vary based on
Nutrients – availability of food sources for bacteria.
Conditions – temperature, pH, oxygen, etc.
Site of formation – where the biofilm grows (e.g., medical device, water pipe, tissue).
Demographics – the types and proportions of bacterial species present.
benefits of biofilms
Wastewater treatment – biofilms help break down pollutants.
Bioremediation – used to clean up oil spills or toxins.
Nitrogen fixation – beneficial soil biofilms support plant growth.
Protection for microbes – helps survival in harsh environments.
Industrial and biotech uses – biofilms can be used in fermentation or bioenergy production.
B-lactose
cleaves/cut the antibiotic coming in making them non effective
metabolically active
efflux pumps
pump the drugs out before they reach their target
metabolically active
when drug enters biofilm
the drug has a very hard time moving and cant find the target
metabolically inactive
no growth or division, decreased uptake of the antibiotics, depletion of antibiotic target
Persister cells:
cells that go dormant when under stress(antibiotics) and wake up when the stress is gone and start reproducing
Extracellular DNA (eDNA)
-there is a lot of nucleic acid in the matrix of biofilm
-eDNA is pivotal to the structure of biofilm
-It acts like a scaffold or glue that helps hold the biofilm together and gives it structural stability.
-interacts w proteins, polysaccharides, and lipids to strengthen the matrix.
horizontal gene transfer “tool box to survive”
-when one bacteria transfers a gene to another bacteria
-only retains if that gene is beneficial
-3 ways to transfer; phage transduction, natural transformation and conjugation(antibiotic resistant)
ubiquitous
means present
susceptible
means dead
strategies to kill persister cells
Antibiotics that kill without needing the bacteria to be active
Small molecules or antimicrobial peptides that can penetrate and kill even dormant cells
What is “cross-talk” in bacterial biofilm formation? Give an example.
Cross-talk is when different signaling pathways interact to coordinate bacterial behavior.
Example: In Comamonas testosteroni, Che (chemotaxis) and Flm (biofilm formation) pathways communicate to link movement with biofilm development.
Biofilm Components:
Microbes: Bacteria, fungi, algae, viruses (less than 10% of mass)
Exopolysaccharides (EPS): Water-soluble sugars like cellulose, alginate, Psl, Pel (major part of matrix)
Proteins: Pili, fimbriae, enzymes, signaling proteins
Extracellular DNA (eDNA): Helps hold the biofilm together
Key point: Most of the biofilm’s mass (>90%) comes from the matrix (EPS, proteins, eDNA), not the microbes themselves.
