202 General Microbiology II

Microbial Ecology Concepts

Ecosystem

Ecosystems are communities of organisms, including their physical and chemical environments.

• Habitat - environment (physical place) in which an organism lives; microbial activities are affected by biological (other organisms and their by-products) and physical (temperature, pH, light, nutrient quality and quantity, oxygen level, etc.) environmental factors
• Niche - abstract concept describing all environmental conditions needed for an organism to maintain a viable population, specifying amounts of each resource required to do so (not a physical place)

Symbiosis

Symbiotic relationships are those in which two or more dissimilar organisms live in close association; may be endosymbiosis or ectosymbiosis

• Parasitism
  • one organism (parasite) benefits, while the other (host) is harmed
  • example - infections that lead to damage of host tissues by the parasite, which causes disease (occurs in plants as well as animals)
• Commensalism
  • association in which one organism (commensal) benefits, while the other (host) is neither helped nor harmed
  • example - Clostridium and other microbes live in the human colon where they benefit from nutrients, warmth and shelter, but generally do not cause disease (normal microbiota)
• Mutualism
  • association in which both organisms (mutuals) benefit
  • examples:
    • Escherichia coli lives in the human colon and benefits from nutrients, warmth and shelter found there, generally not causing disease, but benefiting the host by producing vitamins and preventing growth of harmful microbes
    • lichens - mutualistic associations between a mycobiont (ascomycete) and a phycobiont (green alga or cyanobacterium)
      • mycobiont provides a stable environment (protects from excessive light, supplies water and minerals, provides a firm substrate) within which the phycobiont can grow somewhat free from environmental stress
      • phycobiont provides oxygen, organic carbon, other nutrients for both microbes
      • mostly ectosymbiotic, although some fungi obtain nutrients from their phycobionts using haustoria (projections of hyphae that penetrate the phycobiont cell wall)
    • protozoan symbiosis with bacteria and archaea
      • Personympha (a protozoan that lives in the gut of termites) can digest cellulose only because it has cellulase-producing endosymbiotic bacteria
      • Metopus contortus (an anaerobic cilliated protozoan) has a number of symbiotes
        • two endosymbiotes
          • hydrogenosomes - degenerate bacteria that use pyruvate and NADH (both generated via glycolytic catabolism of the cilliate) to generate CO₂, H₂ and acetate
          • methanogens - use CO₂ and H₂ generated in the hydrogenosomes to generate methane
        • one ectosymbiote - sulfate-reducing bacteria oxidize the acetate generated in the hydrogenosomes to obtain energy via anaerobic respiration and reduce sulfate in the process
      • Strombidium purpureum - anaerobic protozoan that has photosynthetic purple sulfur bacteria living in its cytoplasm and furnishing it with energy
    • rumen ectosymbiosis - cattle, deer, camels, sheep, goats, giraffes have a four-compartment "stomach" (rumen) in which cellulolytic bacteria, fungi and protozoa (~10¹⁰ cells per mL) live
      • large amounts of grass, etc. (containing insoluble polysaccharides and cellulose) are quickly mixed with saliva by perfunctory chewing, then swallowed into the rumen where the food is churned until it becomes a pulpy mass and mixed with the large microbial population which partially digests and anaerobically ferments the food, generating fatty acids (absorbed by bloodstream; used for gluconeogenesis in liver) and vitamins as well as carbon dioxide and methane (2 liters of methane per minute are released by eructation)
      • the food later moves into the reticulum, from which it is regurgitated as a "cud," thoroughly chewed (mixing it with more saliva) and swallowed into the rumen
      • this process continues until the food becomes liquid and flows into the omasum (water absorbed), then into the abomasum (gastric stomach) where the animal's own enzymes digest the microbes from the rumen (supplying amino acids, sugars, etc.) and the remaining food nutrients in the "normal" mammalian way 

Microbes in Nature

Microenvironment

This is the immediate environment of very small organisms.

Surface Attachment

Microbes are generally attached (via glycocalyx) to:

• stones, etc. - especially in moving water
• other living things (frequently symbiotic) - plants or animals
• dead organic matter (saprophytic) 

Nutrients

Nutrients are frequently adsorbed to surfaces; their concentrations are frequently 100-1000X lower than in common laboratory culture media.

Growth Rates

Growth rates are much lower on average in nature than in the laboratory; characterized by "spurts" of exponential growth interspersed with long periods of stationary conditions when nutrients are to dilute for fast growth.

Competition

Competition is due to high population densities and short generation times.

• competition arises when two or more organisms need the same resource and that resource is present in limited amounts
• organism with the shortest generation time frequently "wins" by outgrowing and thus replacing its competitors; this may be mediated by inhibiting the growth of other organisms by secreting antibiotics, toxic substances, etc. into the environment
• local diversity is limited by competition

Food Chains

A food chain is a series of organisms through which energy flows (a food web is a network of interlinked food chains):

• producers - organisms that generate organic compounds using inorganic compounds as sources of carbon, nitrogen, phosphorus, etc. and light (phototrophs) or inorganic chemicals (lithotrophs) as sources of energy
• consumers - organisms (organotrophs) that obtain carbon and energy from organic compounds made by other organisms
  • herbivores "prey" upon producers
  • carnivores prey upon herbivores
  • omnivores prey upon producers, herbivores and carnivores
• decomposers (generally organotrophic microbes) recycle some carbon and energy to other organotrophs (via organic compounds) and inorganic compounds to all organisms (mineralization of organic compounds) via biogeochemical cycles

Communication

Microbes communicate with one another via chemical messages.

• One form of communication is via quorum sensing
  • Bonnie Bassler had the insight needed for she and other scientists to begin working out how bacteria talk to one another.
  • Watch the recent episode of NOVA ScienceNow that featured Dr. Bassler and her work on quorum sensing.
  • Read the transcript about her and her work as featured on NOVA ScienceNow.