4.

• Microbial Ecology


  The study of the interrelationships among microorganisms and the environment
• Microbial adaptations


  • Essential for microbes to survive in different ecological niches
  • Microbes must adapt to constantly varying conditions
• Applied Environmental or Industrial Microbiology

  Use of microbial adaptations to solve environmental problems or challenges
• Examples of Applied Environmental or Industrial Microbiology

  • Bioremediation
  • Clean oil spills
  • Recycling
  • Detoxification
• Macroscopic Life


  Higher trophic levels of organisms are fundamentally simple with regards to metabolics. With gases and nutrients being exchanged largely between photosynthetic and non-photosynthetic organisms.

  
• Microscopic Life


  Responsible for recycling decayed matter under both aerobic and anaerobic conditions. Far more complex than macroscopic systems. Responsible for maintaining regulation of Earth's biogeochemistry.
• Coupled microbial systems


  • Lichen: Fungi+Algae
  • Sulfur bacteria in Riftia
  • Dinoflagellates in flatworm
  • Mycorrhizae

  
• Ecological niche


  The environmental factors which affect the ability of an organism to live and reproduce
• Fundamental Niche


  The range of environmental factors that an organism can survive
• Realized Niche


  The range of factors (including biotic) that a species is actually found
• Horizontal gene transfer


  The process by which genetic material between neighboring bacteria is accomplished through transformation, transduction, or conjugation

  
• Nutrients


  The elements and compounds that organisms need to live, grow, and reproduce
• Biogeochemical cycles


  Global cycles that recycle nutrients through the earth's air, land, water, and organisms
• Carbon Cycle


  Consists of two interconnected subcycles: Fast Cycle (cycling of carbon between the environment and living things) and Slow Cycle (long-term cycling of carbon through geologic processes)

  
• Syntrophy


  The process of one organism living off of the metabolites of another
• Phototrophs


  Dependent on CO2 fixation and recycling of nutrients produced by heterotrophs (via respiration)
• Heterotrophs


  Dependent upon the consumption of organic matter produced by phototrophs (via photosynthesis)
• Carbon fixation


  Capturing CO2 and fixing it for use (via the Calvin Cycle)
• Terrestrial autotrophs


  Predominately capture CO2 gas directly
• Marine autotrophs


  Mostly utilize dissolved CO2 in the form of bicarbonate (HCO3-)
• Significant amounts of carbon are held in soil and fossil forms within the Earth. While some of this CO2 gets released and returned to the atmosphere through microbial decomposition activity and geologic processes like volcanos, human burning of fossil fuels over the least 200+ years has accelerated CO2 release into the atmosphere from these long-term reservoirs.
• CO2 is a greenhouse gas, a gas in the atmosphere which promotes trapping of heat absorbed from the sun. Since the industrial revolution, several scientific studies have shown that there has been a significant increase in atmospheric CO2 levels!
• Methane is 25x stronger of a greenhouse gas than CO2. There are only 2 known metabolic pathways to generate methane: acetate fermentation and methanogenesis (via Archaea). Both happen in cows mediated by microbes!
• Nitrogen Cycle


  A complex biogeochemical cycle where nitrogen is converted from its inert atmospheric molecular form (N2) into forms that are useful in biological processes
• Nitrogen Cycle


  1. Nitrogen Fixation

  2. Nitrification

  3. Denitrification
• Ammonification


  Microbes convert urine and other decomposition/ waste products directly into ammonia
• Rhizosphere


  The immediate area around where soil and roots meet
• Mycorrhizae


  Fungal symbionts that form symbiotic relationships with plants
• There are approximately 1000X more microbes in the rhizosphere than in the rest of the soil. In this region, we find considerable competition, symbioses, dynamic interactions between different organisms.
• Sulfur Cycle


  Involves inter-conversions of sulfur between the atmosphere and terrestrial surfaces
• Sulfur Cycle


  1. Sulfate reduction

  2. Sulfur reduction

  3. Sulfur oxidation
• Phosphorus Cycle


  Largely involves cycling between organic / biologic and inorganic / geologic systems. This cycle does NOT involve a gas phase.
• Phosphorus Cycle


  1. Reservoir Formation

  2. Assimilation

  3. Release / Decomposition
• Microbes mostly play a role in converting organic phosphorus containing compounds back into inorganic phosphorus (phosphates)