Lecture Notes on the Earth Microbiome Project

Introduction

• Historical Context: Leonardo da Vinci noted our limited knowledge about soil compared to celestial bodies.
• Era Context: Pre-dates microscopes, ecology, biochemistry, and germ theory.

The Earth Microbiome Project

• Objective: Systematic study of Earth's smallest life forms to build a comprehensive database.
• Scale: More microbes in a kilogram of soil than stars in the galaxy; 10^30 microbes on Earth vs. 10^24 stars in the universe.
• Importance: Microbes control the carbon cycle, climate, atmosphere, and nutrient cycling.

Microbes

• Definition: Smallest and most abundant life forms.
• Fossil Evidence: Earliest known fossils, 3.4 billion years old from Western Australia.
• Evolution: Multicellular organisms evolved 2 billion years ago.

Unknowns in Microbiology

• Number of microbial species: Estimated between 1 million and 1 billion, vastly more than the 8,000 cultured species.
• Microbial omnipresence: They are found almost everywhere.
• Origins and movements: Unclear how microbes move and inhabit different environments.

Research Methods

• Traditional Culturing: Less than 1% of microbes can be cultured.
• New Approach: Environmental sampling, DNA extraction using robots, and sequencing.
• DNA Sequencing: Producing billions of DNA fragments for reassembly into genomes.

Computational Challenges

• Problem: Reconstructing full genomes from DNA fragments is similar to reconstructing coherent stories from social media posts.
• Solution: Using massive computers (e.g., Mira supercomputer at Argonne) to process and sort data.

Genomic Insights

• Example: Aphid symbiont bacteria with 700 genes providing essential functions.
• ATP Synthase: Smallest rotary motor, essential for energy production.

Complexity of Microbial Life

• Microbes as chemical factories: 4,000 genes per microbe with potential for unique chemical reactions.
• Potential for hundred billion unique proteins and functions.

Global Microbial Distribution

• Transport: Dust grains can carry microbes globally.
• Microbial Comparison: Half of the microbes are common across different global locations.

Intellectual Property and Microbial Research

• Question of whether unique microbes exist globally or locally.
• Implications for accessing and utilizing microbial genetic material.

Project Progress and Future

• Initiated by a group of 25 scientists in 2010.
• Global Collaboration: Growing interest with hundreds of scientists involved.
• Sampling Goal: Potential need for millions of samples using robotic aid.

Conclusion

• Microbiology may surpass astronomy in complexity and intrigue in the near future.

Thank you for attending the lecture.