Chapter Summary


  • Microbial populations fill unique niches in ecosystems. Every environment on Earth (to depths of 3 km below the surface) contains microbes. Every chemical reaction that may yield free energy can be utilized by some kind of microbe.
  • Microbes fix or assimilate essential elements into biomass, which recycles within ecosystems. Important elements, such as nitrogen, are fixed solely by bacteria and archaea.
  • Primary producers fix single-carbon units, usually CO2. Microbial primary producers include algae, cyanobacteria, and lithotrophs.
  • In a food web, consumers catabolize the bodies of producers, generating CO2 and releasing heat energy. Dissimilation is the process of breaking down nutrients to inorganic minerals such as CO2 and NO2, usually through oxidation.
  • Microbial activity depends on levels of oxygen, carbon, nitrogen, and other essential elements, as well as environmental factors such as temperature, salinity, and pH. The largest volume of our biosphere contains anaerobic bacteria and archaea. Beneath Earth’s surface, most metabolism is anaerobic.


  • Symbiosis is an intimate association between organisms of different species.
  • Mutualism is a form of symbiosis in which each partner species benefits from the other. The relationship is usually obligatory for growth of one or both partners.
  • Lichens are a mutualistic community of algae or cyanobacteria with fungi. Lichens are essential producers for dry soil habitats.
  • Termite gut mutualists include cellulose-digesting bacteria and protists. A major by-product is hydrogen gas.
  • Syntrophy is a metabolic association between two species, requiring both partners in order to complete the metabolism with a negative value of ΔG.
  • Parasitism is a form of symbiosis in which one species grows at the expense of another, usually much larger, host organism.


  • The euphotic zone of the ocean is the upper part of the water column that receives light for phototrophs. Below, in the aphotic zone, only heterotrophs and lithotrophs can grow. The benthos includes the region where the water column meets the ocean floor, as well as sediment below the surface.
  • New microbial species are discovered by metagenomic analysis.
  • Plankton are small floating organisms, including swimming microbes. Phytoplankton are phototrophs such as cyanobacteria and algae. Microbial consumers include protists and viruses. Many marine protists are mixotrophs (producers and consumers in one).
  • Picoplankton are measured by fluorescence microscopy. Their biochemical rate of production is measured by uptake of radiolabeled nutrients.
  • Benthic microbes are barophiles. The seafloor supports psychrophiles, whereas hydrothermal vents support thermophiles. Vents and cold seeps support sulfur-oxidizing bacteria, sulfur-reducing bacteria, methanogens, and methanotrophs. Bacteria that oxidize H2S and methane feed symbiotic animals such as tube worms.
  • Aquatic freshwater lakes have stratified water levels. As depth increases, minerals become increasingly reduced. Anaerobic forms of metabolism predominate, with the more favorable alternative electron acceptors used in turn.
  • Lakes may be oligotrophic or eutrophic. Eutrophic lakes may show such high biochemical oxygen demand (BOD) that they cannot support vertebrate life.


  • The uppermost horizons of soil consist of detritus, largely aerated. Below the aerated layers, the eluviated horizon experiences water saturation. Lower layers are anoxic.
  • The soil food web includes a complex range of microbial producers, consumers, predators, decomposers, and mutualists. Microbial mats and biofilms are complex multispecies communities of bacteria, fungi, and other microbes.
  • Fungi decompose lignin, a complex aromatic tree component that is challenging to digest. Lignin decomposition forms humus.
  • Fungi form symbiotic associations with plant roots called mycorrhizae. Mycorrhizae transport soil nutrients among many different kinds of plants.
  • Wetland soils alternate aerated (dry) with anoxic (water-saturated) conditions. Anoxic wetland soil favors methanogenesis. Wetland soils are among the most productive ecosystems.


  • Endophytes are bacteria or fungi that grow within plant transport vessels, conferring benefits such as resistance to pathogens.
  • Rhizobia induce legume roots to nodulate for nitrogen fixation. The bacteria enter the root as infection threads. Some of the bacteria enter root cells and develop into nitrogen-fixing bacteroids.
  • Bacteroids gain energy from plant cell respiration but must remain anaerobic. The anaerobic state is protected by the oxygen-binding protein leghemoglobin.
  • Plant pathogens include bacteria, fungi, and viruses. Some pathogens only mildly affect the plant, whereas others cause devastation.
  • Fungi invade plants using haustoria. The haustoria grow into the plant cell by penetrating the cell wall and invaginating the cell membrane to avoid leakage of cytoplasm.


  • Animals harbor microbial communities. Microbes populate the skin, where they provide protection from pathogens. Other species grow in the animal’s digestive system, where they enhance nutrition.
  • Corals and sea anemones harbor zooxanthellae, algae that provide products of photosynthesis in exchange for a protected habitat.
  • The rumen of ruminant animals is a complex microbial digestive chamber. Rumen microbes, including bacteria, protists, and fungi, digest complex plant materials. The microbial digestion generates short-chain fatty acids that are absorbed by the intestinal lining.
  • Foregut and hindgut fermentation contribute to digestion in many vertebrate animals, including humans.