Lesson 1 Blaser et al., 2016

Environmental Biotechnology

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🌍 Microbes: The Hidden Architects of Earth

Microbes have shaped Earth for 3.5+ billion years.
They caused the Great Oxidation Event 🌬️, enabling multicellular life.
Eukaryotes rely on microbes: mitochondria ⚡ and chloroplasts 🌱 are ancient bacteria!
They drive the carbon cycle (plankton fixing ~50% of CO₂ each year) and nitrogen fixation 🌾, which powered ecosystems long before Haber-Bosch.

⚠️ Big 21st-Century Challenges

Human activity → climate change 🌡️, soil degradation, water shortages 💧, and urbanization 🏙️.
By 2050, 70% of humans will live in cities, encountering new built-environment microbiomes.
Microbes affect greenhouse gases (CO₂, CH₄, N₂O) and disasters like toxic algal blooms 💀.

🧑‍⚕️ Microbiomes and Human Health

Gut microbiota linked to malnutrition, obesity, diabetes 🍔 and even brain/behavior 🧠.
Early-life microbiome disruptions → allergies, asthma, autoimmune diseases 🤧.
Antibiotics + industrial lifestyles may reduce essential co-evolved microbes.

🌱 Agriculture, Industry, and Society

Crops: Soil microbes help plants get nutrients + resist pests 🐛.
Chemistry: Microbes are “Earth’s master chemists” 🧪, making antibiotics, hormones, fuels, detergents, etc.
Dark matter: Most microbial diversity is unknown 👻. Genomics reveals endless hidden genes.

🛠️ Roadblocks to Microbiome Science

DNA sequencing ≠ function. We need ways to decode unknown genes 🧬.
Scaling problem: sequencing outpaces our ability to test gene functions.
Environments are complex: microbes live in micron-scale gradients we usually overlook.
Bias & standardization issues: sample processing can distort results.

🔮 What We Need

Tools to test causality, not just correlation (e.g., CRISPR in microbes ✂️).
Synthetic communities to study interactions.
Models spanning electron transfer ⚡ → ecosystems 🌊 → Earth system 🌍.
Portable genome analysis tools (sequencing in the field).
Collaboration across disciplines, like the Human Genome Project.

🌐 A Unified Microbiome Initiative (UMI)

A global effort to map, predict, and harness microbiomes responsibly.
Potential benefits:
- Sustainable agriculture 🌾
- Bio-based fuels & chemicals ⛽
- Pollution cleanup 🧹
- Health interventions 🩺
But: raises ethical, legal, and social issues (regulation, risks, definitions of “healthy”).

Microbiomes = key to food, health, environment, and energy. To truly harness them, we need predictive, interdisciplinary science + careful governance. Like the Human Genome Project, a UMI could transform both science and society 🚀.

Quiz

Score: 0/30 (0%)

Q0. Which event marked the first major oxygenation of Earth's atmosphere caused by microbes?

Cambrian Explosion

Great Oxidation Event

Permian Extinction

Carboniferous Expansion

Q1. What do mitochondria and chloroplasts have in common evolutionarily?

They both evolved from ancient viruses

They are modified ribosomes

They originated from once free-living bacteria

They evolved independently within eukaryotic cells

Q2. Which process replaced biological nitrogen fixation as the dominant source of nitrogen for agriculture in the 20th century?

Haber-Bosch process

Calvin Cycle

Denitrification

Nitrification

Q3. Which greenhouse gas is mainly produced by microbial activity in rice paddies and livestock?

Nitrous oxide (N2O)

Methane (CH4)

Carbon dioxide (CO2)

Sulfur dioxide (SO2)

Q4. What is the estimated percentage of humans expected to live in cities by 2050?

40%

55%

70%

85%

Q5. Which microbial function is primarily responsible for purifying water and recycling nutrients in aquatic ecosystems?

Nitrogen fixation

Photosynthesis

Decomposition and nutrient cycling

Fermentation

Q6. What are metatranscriptomics and metaproteomics used for in microbiome research?

To visualize microbes

To sequence DNA

To study gene expression and protein function in communities

To cultivate unknown microbes

Q7. Which of the following describes 'microbial dark matter'?

Unknown viruses in the ocean

Microbial species known only through DNA sequences, not cultures

Extinct microbes

Fossilized microbial mats

Q8. What is one key limitation of current microbiome sequencing technologies?

High error rates in DNA replication

Sequencing provides potential function, not actual activity

DNA cannot be extracted from most microbes

They cannot identify eukaryotic genes

Q9. What is the goal of the proposed Unified Microbiome Initiative (UMI)?

To study only human gut microbes

To coordinate global research to understand and harness microbiomes

To regulate antibiotic use

To replace the Human Genome Project

Q10. Which analytical technique allows label-free detection of chemical bonds in microbial samples?

Fluorescence microscopy

Fourier transform infrared (FTIR) spectromicroscopy

Gel electrophoresis

Mass spectrometry imaging

Q11. Which of these is a major source of bias in microbiome studies?

DNA extraction method variability

Temperature fluctuations during sequencing

Sample labeling errors

PCR-free sequencing

Q12. Why is homogenizing soil samples problematic for microbial studies?

It kills anaerobes

It destroys micron-scale heterogeneity crucial to microbial function

It mixes organic matter unevenly

It changes soil pH

Q13. Which gene-editing technology allows targeted manipulation of microbial genes in communities?

siRNA

CRISPR/Cas9

Transposon sequencing

RNA interference

Q14. What was one key ethical concern raised by the authors about microbiome manipulation?

Microbiomes may evolve or cross borders, complicating regulation

It will increase fossil fuel use

It may lead to extinction of eukaryotes

It will reduce biodiversity

Q15. Microbes were responsible for Earth's Great Oxidation Event.

True

False

Q16. The Haber–Bosch process is an energy-efficient biological method for nitrogen fixation.

True

False

Q17. The majority of microbes on Earth have been successfully cultured in laboratories.

True

False

Q18. Urban environments tend to have microbial communities largely derived from human occupants.

True

False

Q19. Microbial activity can both store and release carbon from soils, influencing climate feedbacks.

True

False

Q20. Metabolomics focuses on sequencing microbial genomes.

True

False

Q21. The Unified Microbiome Initiative (UMI) was proposed to unify research across human, plant, and environmental microbiomes.

True

False

Q22. Microbes contribute to both methane and nitrous oxide emissions from agriculture.

True

False

Q23. DNA sequencing alone can fully determine microbial activity and ecosystem function.

True

False

Q24. Microbial communities can be engineered to produce biofuels and industrial chemicals.

True

False

Q25. Homogenizing environmental samples improves the resolution of microbial spatial structure.

True

False

Q26. CRISPR/Cas9 can be used to test causation in microbial networks by selectively removing genes or species.

True

False

Q27. Ethical and regulatory frameworks for microbiome research are already fully established worldwide.

True

False

Q28. Microbes are essential to the nitrogen cycle but play no role in carbon cycling.

True

False

Q29. The authors compare the need for a unified microbiome effort to the Human Genome Project.

True

False