Chapter Summary


  • Microbes cycle essential elements in the biosphere. Many key cycling reactions are performed only by bacteria and archaea.
  • Elements cycle between organisms and abiotic sources and sinks. The most accessible source of carbon and nitrogen is the atmosphere. The Earth’s crust stores large amounts of key elements, but their availability to organisms is limited.
  • Environmental flux of elements is measured through chemistry. Methods include infrared and mass spectroscopy, gas chromatography, radioisotope incorporation, and the measurement of isotope ratios


  • The most accessible reservoir for carbon is the atmosphere (CO2). Atmospheric carbon is severely perturbed by the burning of fossil fuels.
  • Cyanobacteria and other phytoplankton cycle much of the CO2 in the biosphere. Oxygen released by phototrophs is used by aerobic heterotrophs and lithotrophs.
  • Carbon cycling is linked to the cycling of hydrogen and oxygen.
  • Anaerobic environments cycle carbon through bacteria and archaea. Bacteria conduct fermentation and anaerobic respiration. Methanogens release methane, much of which is removed by methaneoxidizing bacteria and archaea.
  • Microbial decomposition returns CO2 to the atmosphere. Microbial decomposition is a major contributor to the accelerated CO2 flux associated with deforestation.


  • The hydrologic cycle is the cyclic exchange of water between the atmosphere and the biosphere. Water precipitates as rain, which enters the ground and ultimately flows to the oceans. Along the way, water evaporates, returning to the atmosphere.
  • Water carries organic carbon that generates biochemical oxygen demand (BOD). High BOD accelerates heterotrophic respiration and depletes oxygen needed by fish.
  • Wastewater treatment cuts down BOD. Secondary treatment involves microbial communities that decompose the soluble organic content.
  • Wetlands filter water naturally. Wetland filtration helps purify groundwater entering aquifers


  • Nitrogen in ecosystems is found in a wide range of oxidation states. Interconversion of most of these states requires prokaryotes.
  • The main source and sink of nitrogen is the atmosphere. Nitrogen gas is fixed into ammonium ion by some bacteria and archaea. Denitrifying bacteria reduce NO3– successively back to N2 and return it to the atmosphere.
  • Nitrogen fixation is conducted by symbiotic bacteria in association with specific plants. Legume-associated nitrogen fixation is critical for agriculture.
  • Nitrification is aerobic oxidation of ammonia to nitrite and nitrate. Nitrification yields energy for lithotrophic bacteria in soil and water.
  • Nitrate can be reduced to ammonia under anoxic conditions. Especially in the deep ocean, NO3– may be reduced by hydrogen gas to ammonia.
  • Ammonium is oxidized by the anammox reaction. Anaerobic ammonium oxidation accounts for a large part of all N2 returned to the atmosphere.


  • Sulfate is abundant in marine water.
  • Oxidized and reduced forms of sulfur are cycled in ecosystems. Sulfate and sulfite serve as electron acceptors for respiration. Hydrogen sulfide serves as an electron donor. Sulfur cycling participates in acid mine drainage and pipe erosion.
  • Phosphorus cycles primarily in the fully oxidized form (phosphate). Phosphate limits growth of phototrophic bacteria and algae in some aquatic and marine systems.
  • Iron cycles in oxidized and reduced forms. Oxidized iron (Fe3+) serves as a terminal electron acceptor in anaerobic soil and water. Reduced iron (Fe2+) from rock is oxidized through weathering or mining. Bacterial lithotrophy accelerates iron oxidation, leading to acidification.
  • Metal toxins can be metabolized by bacteria. Bacterial metabolism may either increase or decrease toxicity.
  • Marine habitats show resource colimitation. Multiple resources may be limiting for the phytoplankton community or for different populations.


  • Astrobiology is the study of life in the universe, including possible habitats outside Earth.
  • The search for extraterrestrial life is based on methods similar to those used to seek early life on Earth. Evidence includes chemical and physical biosignatures, isotope ratios, microfossils, and metabolic activity.
  • Mars is the planet whose geology most closely resembles that of Earth. Geological features strongly support the past existence of flowing water, a prerequisite for microbial life.
  • Jupiter’s moon Europa is proposed as another possible site for life. Europa is bathed in a sea of brine similar to terrestrial habitats for halophiles.