🧬 Part I: Biofilms

1️⃣ Introduction

Environmental biotechnology studies mixed microbial communities driving nutrient cycles. These communities form biofilms — surface-attached, structured groups of microbes surrounded by self-produced extracellular polymeric substances (EPS).

2️⃣ Growth forms of bacteria

Bacteria can live:

• 🧍‍♂️ As free cells (planktonic)
• 🧩 In flocs (loose aggregates)
• 🧱 On surfaces (biofilms) — the most successful lifestyle, found in nearly every environment.

3️⃣ Biofilms everywhere!

Examples:

• Sea ice: Psychrophiles (cold-loving)
• Deep-sea vents: Thermophiles, barophiles
• Sulfuric springs: Acidophiles
• Salt lakes: Halophiles
• Soda lakes: Alkalophiles

Biofilms even grow in unexpected or “beautiful” places — like rocks in streams (epilithic biofilms) 🌊.

4️⃣ Human biofilms 🧠🦷

Biofilms cause:

• Dental plaque
• Urinary catheter infections
• Contact lens contamination
• Implant infections (e.g., artificial hearts)

They’re also vital in wastewater treatment, bioenergy, and biosolid production — but harmful in biofouling and industrial corrosion.

5️⃣ EPS: Extracellular Polymeric Substances 🧪

EPS form the “house” of biofilm cells. They include:

• Polysaccharides
• Proteins & glycoproteins
• Lipids
• Nucleic acids
• Humic substances

EPS provide structure, stability, nutrient recycling, and protection from toxins. Cells can control EPS composition — changing charge, hydrophobicity, or chain length to adapt.

6️⃣ Biofilm matrix genes 🧬

EPS production is genetically encoded via gene clusters for: Alginate, Cellulose, Colanic acid, Diutan, Hyaluronic acid, Pel, Psl, Succinoglycan, Xanthan.

7️⃣ Amyloids in biofilms 🧫

Amyloids are fibril proteins (3–10 nm) with β-sheet structures:

• Functional amyloids: strengthen biofilms (e.g., in bacteria or fungi)
• Pathological amyloids: cause diseases (Alzheimer’s, Parkinson’s, prion diseases)

They bind dyes like Congo Red and Thioflavin T.

8️⃣ Biofilm architecture 🧩

Structure is complex — microcolonies, channels, and fronds allow water and nutrient flow. Protozoa and amoebae interact dynamically with bacterial colonies. Biofilms are open, living ecosystems with predator–prey interactions.

9️⃣ Quorum sensing & communication 📡

Bacteria use chemical signals (e.g., N-acyl homoserine lactones) to coordinate behavior — biofilm growth, virulence, and dispersal — but only when cell density is high (“quorum”).

🔟 Predation & defense ⚔️

Biofilms face attacks from:

• Protozoa & ciliates
• Competing bacteria (e.g., Vampirococcus)
• Viruses (bacteriophages)

They fight back using:

• Vesicles containing enzymes and DNA (“killer vesicles”)
• Antibiotics as microbial weapons

1️⃣1️⃣ Biofilms & microbial communities 🌍

Microbes function as communal metabolisms — sharing nutrients and electrons to drive biogeochemical cycles (carbon, nitrogen, sulfur). Shift from viewing “individual metabolism” → “community metabolism.”

🧫 Part II: One Health & Antibiotic Resistance Genes (ARGs)

1️⃣2️⃣ One Health 🌎

An integrated concept linking human, animal, and environmental health. Diseases, microbiota, and antibiotic resistance travel across these systems. → Environmental problems become medical problems.

1️⃣3️⃣ Antibiotic Resistance Crisis ⚠️

• In 2019: 1.27 million deaths directly caused by resistant bacteria.
• Projected to surpass cancer deaths by 2050. Resistance spreads faster than new drugs are developed.

1️⃣4️⃣ Antibiotics basics 💊

• Therapeutic: treat infections
• Prophylactic: prevent infection (in animals)
• Growth promotion: boost livestock yield (now banned in EU)

Antibiotics act by blocking:

1. Cell wall synthesis
2. DNA/RNA replication
3. Protein synthesis
4. Metabolism
5. Cell membrane integrity

They are bacteriostatic (stop growth) or bactericidal (kill).

1️⃣5️⃣ Origins of antibiotics 🌿

Many come from soil bacteria (Streptomyces) or fungi. Example:

• Penicillin (fungus)
• Polymyxins (Gram-positive bacteria)

Because of natural diversity, bacteria evolved numerous defense mechanisms → ARGs.

1️⃣6️⃣ Mechanisms of resistance 🧬

1. Enzymatic degradation (e.g., β-lactamase breaks penicillin ring)
2. Target modification (mutate ribosome or enzyme)
3. Efflux pumps (remove antibiotics from cell)
4. Reduced permeability (change porins)

Genes like sul1, mcr-1, tetM, vanA encode these mechanisms. The total pool of resistance genes in an environment is the resistome.

1️⃣7️⃣ Ancient origins 🏔️

ARGs existed long before humans:

• Found in 30,000-year-old permafrost
• Antarctic soils
• Isolated Amazon tribes

So resistance is natural, but human misuse amplifies it.

1️⃣8️⃣ How resistance spreads 🚀

• Mutations (spontaneous or damage-induced)
• Horizontal Gene Transfer (HGT): DNA transfer via plasmids, transposons, or phages → enables rapid spread across species and environments.

1️⃣9️⃣ Environment as ARG reservoir 🌊

Antibiotics and resistance genes move between:

• Wastewater, soil, and manure
• Wildlife and humans
• Global travel and trade

Hotspots include:

• Wastewater plants
• Animal farms
• Hospitals
• Aquaculture

2️⃣0️⃣ Bioremediation & ARG monitoring 🧫

Some microbes even degrade antibiotics (e.g., Arthrobacter D2 can eat sulfonamides). Surveillance uses:

• Culture-dependent (disk diffusion, AST)
• Culture-independent (PCR, WGS, metagenomics) → Metagenomics detects known and novel ARGs.

2️⃣1️⃣ Global monitoring 🌐

WHO’s GLASS (Global Antimicrobial Resistance Surveillance System) tracks resistance in:

• Humans
• Food chain
• Environment

Goals: awareness, research, infection prevention, drug optimization, sustainable funding.

2️⃣2️⃣ Denmark case study 🇩🇰

“Microflora Danica” mapped 10,000 environmental samples. Findings:

• ARGs lowest in sediments, highest in sewage
• Salinity reduces ARGs
• Water treatment effectively lowers resistance Danish wastewater and livestock show lower ARG levels than international averages.

2️⃣3️⃣ Challenges 🧩

1. No standardized global methods
2. Sampling variation (time & space)
3. Diverse matrices (soil, water, sludge)
4. Viability vs. gene detection mismatch
5. Translating abundance → actual risk
6. Distinguishing natural vs. anthropogenic ARGs
7. Need cross-sector collaboration
8. Funding and communication gaps

2️⃣4️⃣ Solutions 💡

• New antibiotics and phage therapy
• Collateral sensitivity: some resistances make bacteria vulnerable to other drugs → e.g., β-lactamase inhibitors resensitize MRSA
• Combination therapy prevents resistance
• Behavioral change & awareness campaigns

🧭 Main takeaway

“Biofilms are the planet’s dominant microbial form, and antibiotic resistance is a natural but amplified outcome of microbial survival strategies. Managing ARGs demands a One Health approach linking humans, animals, and environments.” 🌍🧫💊