Environmental Bacteria and Microbiomes

Environmental DNA Sequencing

• Norm Pace's approach: Extract DNA directly from the environment (e.g., boiling sulfur springs) without culturing organisms.
• Graduate students collect samples from extreme environments.
• DNA is purified using methods like nitrocellulose columns due to its sticky nature.
• Carl Woese's sequencing technique to compare DNA sequences.

Discoveries from Environmental Sequencing

• Early findings revealed DNA sequences drastically different from known cultured bacteria.
• These sequences, while bacterial, represented previously unknown groups.
• Visualization: Cultured groups (dark black) vs. DNA-only known groups (gray).
• Early 2000s: Half of the known bacteria came from cultured samples, half only from DNA sequences.
• Within a few years, the majority of bacterial knowledge came from DNA sequencing of environmental samples.

Implications of Findings

• "Reality astonishes theory": Environmental DNA revealed a vast diversity beyond cultured organisms.
• Pathogens represent only a tiny fraction of bacterial diversity.
• Most bacteria are distinct from pathogens, with unknown functions.
• Genomic analysis provides clues to bacterial capabilities (e.g., genes for glucose use, photosynthesis).
• Presence of a gene does not guarantee its expression.

Nutrient Cycling and Microbial Roles

• Microorganisms are key to nutrient cycles, transforming chemicals.
• Microbes establish and maintain the environments in which other organisms live.
• Bacterial photosynthesis led to the presence of oxygen on Earth.

Biogeography of Microbes

• Norm Pace's projects: Soil samples collected across the US to analyze bacterial populations.
• Bacterial populations are influenced by climate and environmental factors.
• Microbes are found in the air, potentially metabolically active in clouds.
• Most bacteria are not pathogens.
• Microbes are found everywhere, including the bottom of the ocean floor

Factors Determining Microbial Presence

• Environmental conditions primarily determine which bacteria thrive in a location.
• High bacterial populations and reproductive rates mean bacteria are virtually everywhere.

Nutrient Cycles

• Driven by geothermal processes and the activity of organisms.
• Microorganisms, especially bacteria, play a primary role in chemical movement.
• Cycles of chemicals are driven by microorganisms.

Focus on Seven Well-Studied Bacterial Groups

• Knowledge mainly comes from what can be grown and examined in the lab.
• These represent only a small fraction of bacterial diversity.
• Genetic diversity within bacteria is greater than that among all eukaryotes.

Proteobacteria

• Largest defined clade of bacteria, including both cultured and uncultured species.
• Contains many known pathogens (e.g., cholera, E. coli, Salmonella, gonorrhea).
• Also includes many non-pathogenic bacteria.

Bacterial Structure and Cell Walls

• Monoderm (Gram-positive) and diderm (Gram-negative) bacteria share common features.
• Peptidoglycan cell wall: synapomorphic trait of bacteria.
• Peptidoglycan protects against osmotic pressure changes.
• Differences in cell wall structure influence staining.

Antibiotics and Selective Toxicity

• Antibiotics target molecules produced by bacteria but not by eukaryotes.
• Peptidoglycan is a prime antibiotic target; its disruption causes cells to burst.

Multicellularity and Biofilms

• Most bacteria live in biofilms rather than as plankton (free-floating).
• Biofilms: Bacteria adhere to surfaces, secrete an extracellular matrix, and form a community.
• Multicellular behavior involves coordinated responses among bacteria.

Biofilms and Pathogenesis

• Pathogens often form biofilms during infection, coordinating attacks on the host.
• Example: Pseudomonas aeruginosa in cystic fibrosis (CF) patients.
• In CF, sticky mucus in the lungs promotes persistent biofilm formation.
• These lung infections are a major cause of mortality in CF patients.

Biofilm Resistance

• Water channels within biofilms allow nutrients to penetrate and antibiotics to be flushed.
• The extracellular matrix protects bacteria from antibiotics and the host's immune system.
• Biofilms on implanted medical devices can lead to chronic infections.

Biofilm Prevention

• Engineering surfaces to prevent initial bacterial attachment prevents biofilm formation.
• Examples: Microban-treated diaper changing stations.

Advantages of Biofilms

• Protection from chemicals (e.g., antibiotics).
• Avoidance of predators.

The Microbiome

• All microorganisms living in or on another organism's body.
• Examples: Human microbiome, plant microbiome.
• Research is still in the early stages.

Microbiome Treatment: Fecal Transplants

• Clostridium difficile (C. diff) infection: Causes severe diarrhea and colon inflammation.
• Often occurs after antibiotic treatment, which disrupts normal gut bacteria.
• C. diff takes advantage of the reduced diversity and proliferates.

Fecal Microbiota Transplantation (FMT)

• FMT: Transplanting fecal matter from a healthy donor into a patient with recurrent C. diff.
• More effective than antibiotics for recurrent C. diff.
• FMT restores normal bacterial diversity in the colon.

Microbiome Diversity and Health

• Reduced microbiome is associated with several disease states.