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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.