🌱 1. The Hidden World of Microbes

Diversity explosion

• Around 2014, scientists knew ~16 bacterial phyla.
• Now, we know ~150 phyla, showing how much microbial diversity has expanded!
• Yet, even with this progress, most microbes remain undiscovered — perhaps millions or even billions of species exist.

The Microflora Danica Project 🇩🇰

• A major Danish research effort mapping all microbes in Denmark.
• Uses DNA signatures (unique genetic fingerprints) to detect and classify microbes.
• They have already identified ~500,000 microbial species in Denmark and named 1,000 new ones.
  • Names are created by Latinizing nearby town names, e.g., Aalborgensis.
• Despite these advances, most microbes remain unknown and unnamed.

🧫 2. Microbial Evolution and Importance

• Earth: ~4 billion years old.
• For the first 3 billion years, only microbes existed — they ruled the planet!
• Eukaryotes appeared only ~800 million years ago.
• Many microbes evolved to become host-dependent, living with animals or humans.
• If every animal species has one unique microbe, that alone could be 10+ million microbial species.

🧬 3. Molecular Methods to Study Microbes

a) 16S rRNA gene fingerprinting

• The 16S rRNA gene is like a barcode for bacteria.
• Used to identify and estimate microbial diversity in samples (e.g., soil, water).
• Doesn’t require full genome sequencing — cheaper and faster.

b) Genomics

• Sequencing the entire genome of a single microbe.
• Allows identification, classification, and prediction of metabolic potential (what a microbe can do).
• Example: finding genes for nitrogen fixation or toxin degradation.

c) Metagenomics

• Sequencing mixed DNA from whole communities (many species together).
• Tells us who is there and what genes are present — powerful for environmental studies.

d) Meta-transcriptomics / Meta-proteomics / Metabolomics

• Go beyond DNA:
  • 🧬 Metatranscriptomics = study of RNA (which genes are active).
  • 🧫 Metaproteomics = study of proteins (what’s being produced).
  • 💧 Metabolomics = study of metabolites (the chemical products).
• Together, they reveal the functioning ecosystem — not just its genetic potential.

e) Single-cell methods & FISH

• Study individual bacterial cells using microscopy.
• FISH (Fluorescent In Situ Hybridization) uses fluorescent probes to visualize specific microbes directly.
• Useful for locating bacteria and studying their activity inside biofilms or tissues.

💧 4. Microbial Communities and Environmental Engineering

a) Activated sludge systems

• Used in wastewater treatment.
• Example: Singapore’s advanced water reuse system turned wastewater into drinkable water (though people hesitated to drink it).
• Solution: mix it into reservoirs for natural polishing before reuse.

b) Phosphorus recovery ♻️

• Phosphorus (P) = vital fertilizer nutrient.
• Europe has no natural P deposits — depends on imports (US, China, N. Africa).
• Certain bacteria (polyphosphate-accumulating organisms) store P inside their cells.
• These can be used to recover P from wastewater → sustainable fertilizer.
• Some bacteria even make bioplastics from stored polymers — environmentally friendly alternatives!

🔁 5. The Carbon Cycle & Microbial Respiration

Key idea: microbes recycle carbon! 🌿➡️💨

• Plants fix CO₂ into organic matter.
• Microbes decompose this material back into CO₂, closing the cycle.
• Hydrolysis → Respiration → CO₂.

Electron acceptors in respiration:

When microbes break down organics, they use available electron acceptors in order of energy yield:

💡 The deeper you go into sediment or biofilm → less oxygen → microbes switch to alternative acceptors.

⚡ 6. Energy, Redox, and Electron Transfers

Redox basics:

• Oxidation = losing electrons.
• Reduction = gaining electrons.
• Energy is released when electrons move from high-energy donors to low-energy acceptors.
• Example:
  • Fat molecules are highly reduced (many electrons) → great energy source.
  • Oxygen is a powerful acceptor (ends up as H₂O).

Common redox pairs:

⚖️ The electron tower explains why some processes yield more energy than others — the further the electrons “fall,” the more energy released.

🧠 7. Diffusion and Energy Balance

• The type and size of electron acceptors affect how fast they diffuse into microbial cells.
  • O₂ diffuses easily and yields lots of energy.
  • Nitrate needs more molecules to handle the same number of electrons.
  • Iron ions diffuse poorly, limiting reaction speed.
• This helps explain microbial layering in sediments:
  • Oxygen on top,
  • Nitrate and metals in the middle,
  • Sulfate and methane producers deeper down.

🧩 8. Summary of Core Concepts

• 🌍 Microbes dominate Earth’s diversity and drive global biogeochemical cycles.
• 🧬 Modern tools (genomics, metagenomics, metabolomics) reveal both identity and function.
• ♻️ Environmental microbiology applies these insights to wastewater treatment, nutrient recovery, and bioplastic production.
• ⚡ Microbial respiration and redox processes underpin energy flow and matter recycling in ecosystems.