Biol 457 Exam 2

• What is microbial ecology?

  The science that explores interrelationships between organisms and their living and abiotic environment.
• What is environmental microbiology?

  The study of microbial fate and activity in air, water and soil, and the resulting impact on human health and welfare.

  The study of microbes within all habitats, and their beneficial and detrimental impacts on human health and welfare.
• What is the driving force behind environmental microbiology?

  How can we use our understanding of environmental microbiology to benefit society?
• What makes up the environment? What is common in all of these settings?

  Soil, water, air, plants, animals.

  Anthropogenic environments- bioreactors, water treatment plants, waste ponds, houses..

   

  All of these environments have microbial communities that are essential to the way the environment functions.
• What are the core concepts in environmental microbiology?

  1. Ecology, physiology, habitat diversity, thermodynamics, and evolution all need to be considered.
  2. 1' objective for MO is survival, maintenance, generation of ATP, and sporadic growth - DIVIDE.
  3. There is a link between the planet's habitat diversity and what is recorded in the microbial genome.
  4. Advances in EM depend on convergence of many measurements.
  5. Dynamic and methods limited.
• What is biogeochemistry and how does it relate to environmental microbiology?

  ...the study of biological controls on the chemistry of the environment and geochemical regulation of ecological structure and function.

   

  Because natural cycles are regulated by microbes.
• How do microbes act as biogeochemical agents?

  Microbes play critical roles in energy transformations and biogeochemical processes that result in the cycling of elements to living systems.
• What are traits that make microbes act as geochemical agents?

  1.rapid growth and cell division.

  1. many individuals on which natural selection can act.

  2. metabolic diversity.

  3. infallible

  1. have ability to go dormant

  4. ubiquitous

  1. wide range of tolerance to various environmental conditions.

  5. alter environment as a byproduct of metabolic activity

  1. 02 rich atmosphere a direct result of microbial metabolic activity.
• What made up the origin of metabolic pathways?

  First: obligate heterotrophs — small organic molecules (CH3COOH) converted to C02 and CH4.

  Became more complicated... methanogenesis, sulphate  reduction.

   

  S-based photosynthesis... Used hydrogen sulfur instead of water.

  Oldest photosynthesis formula.

   

  02- producing photosynthesis…

  Uses water and makes oxygen.
• What was significant for life on earth to evolve further?

  Formation of O2 rich atmosphere
• What happened during the great oxidation event?

  Reducing atmosphere.

  No production of 02.

  Atmosphere was CO2 and methane, no oxygen. Full of reduced gases.

  
  

  Production of O2 by cyanobacteria.

  Absorption in oceans and seabed rock.

  
  

  Start to see the rise of oxygen.

  Outgassing of 02 from oceans.

  Absorption in lithosphere.

  
  

  Oxidation of methane to C02 and water.

  Evolution of new aerobic life forms.

  Oxidative processes in all geospheres.
• How did oxygen levels change depending on temperatures?

  Microbes oxidize iron, iron falls of the bottom of the water. High temps.

   

  Low oxygen, cyanobacteria cannot make oxygen, not iron layer, now si layer. Low temps.
• What was the great oxidation event?

  Not just as simple as 02 building up in atmosphere.

  Rate of 02 generation must be more than that of injection of reduced gases by volcanoes.

  Reduction of reduced gases and/or removal of H to space.

  Decomposition of organic material on seafloor removes 02 from water and atmosphere, but if it is buried, it is not decomposed.

  SO.. Perhaps a sudden buildup in burial rates allowed 02 to accumulate in atmosphere
• What was the nickel famine?

  Earth used to have 400x nickel that what we have now. Methanogens love nickel to make methane.

  There was a big loss of nickel, so methanogens cannot make methane, so atmosphere gets reduces.
• What are three hypotheses for how the atmosphere got oxygenated?

  1. Iron oxide on seafloor.
  2. Hydrogen going into mantle.
  3. Methanogens cannot make more methane.
• How did the presence of oxygen change metabolic pathways?

  Presence of 02 allowed the development variety of other metabolic pathways — in all cases metabolic energy is obtained from flow of electrons between oxidized or reduced states.
• What are three fates of microbes interacting with the environment?

  1. Ecological success

  ATP generation, nutrient uptake, growth, motility, chemotaxis, photosynthesis (if autotroph).

   

  2. Survival/maintenance

  Quiescence, dormancy, sporulation.

   

  3. Ecological failure

  Starvation, death, autolysis, oxidative stress, competition, predation, parasitism, washout.
• WHat is the difference between species richness and abundance?

  Species richness: the total number of different species present.

  Species abundance: the proportion of each species in an ecosystem.
• What are some important general ecological terms?

  Ecosystem: The sum total of all organisms and abiotic factors in a particular environment.

   

  Habitat: Portion of an ecosystem where a community could reside.

   

  Guilds: Metabolically related microbial populations.

  Sets of guilds form microbial communities that interact with macroorganisms and abiotic factors in the ecosystem.

   

  Niche: Habitat shared by a guild.

  Supplies nutrients as well as conditions for growth.
• How do organisms do in different environments?

  Light = phototroph thrives

  Some light = phototroph survives

  No light = phototroph dies

   

  Inorganic carbon eaters thrive anywhere.

  Organic carbon eaters thrive in soil, sediment, and subsurface sediment but survive in ocean and lake.
• What is aerobic respiration?

  General equation:

  (C6H1206)+ (02) --> 6(C02) + 6(H20)

   

  Shows complete oxidation (ie. all substrate goes to production of C02).

  Some substrate is used to build cell mass, some oxidized to provide NRG.

  O2 is the terminal electron acceptor.

   

  Oxidation, burning, or respiring of sugar.
• What happens to the sugar and oxygen in aerobic respiration?

  Sugar gets oxidized. Oxygen gets reduced.
• Why is aerobic respiration important?

  Dominant mode of growth in oxygenated ecosystems.

  Cycling of carbon (decomposition of dead biomass; assimilation of carbon into new biomass).

  Removes oxygen from groundwaters and surface sediments (allows anaerobic respiration to proceed).

  Produces simple organic carbon molecules that can be used by anaerobes and other organisms.

   

  Aerobic respiration is an efficient way of making energy.
• How does red-ox occur in nature?

  Red-ox indicates the amount of 02 available It is measured as the potential flow of electrons.

  Red-ox drops as heterotrophic organisms consume organic C and 02.
• How does red-ox change based on carbon present?

  Red-ox is very patchy.... both temporally and spatially.

  If there is abundant organic C present, strong red-ox gradients can exist in 2 mm of sediment.

  As progressively lower red-ox potential are achieved, different red-ox reactions dominate.

  Each rxn uses different C sources and different metabolism.
• How does energy yield change throughout the red-ox table?

  There is a declining metabolic yield as you move into lower red-ox metabolisms.

  Low energy yields account for the inefficiency of anaerobic metabolism and preservation of organic matter in sediments.

  At any red-ox potential, the microbial community conducting the metabolism with greatest energy yield will usually out compete the rest.
• What is anaerobic respiration?

  General equation:

  (C6H1206) + alternate TEA --> diverse products

   

  Use TEA's other than 02.

  Nitrate (N03-), ferric iron (Fe3+), sulfate (S042-), carbonate (C032-), certain organic compounds.

  Anaerobes (hate oxygen/dying), aerotolerants (oxygen tolerant/surviving), facultatives (okay with whatever/surviving).

  Energy produced is less than aerobic respiration.
• How is nitrogen reduced in redox?

  Reduction of 02 i.e. aerobic respiration.

  Reduction of nitrate at 747mV (all examples are at pH 7).

  
  

  2N03- + 6H+ + 6e- <> N2 + 3H20 -denitrification
• How is manganese reduced in redox?

  Reduction of manganese at 526 mV.

  Mn02 + 4H+ + 2e- <> Mn+2 + 21-420

   

  Denitrifies and Mn reducers are facultative anaerobes.

  Hydrogen becomes oxidized, Mn is reduced.
• How is iron reduced in redox?

  Reduction of iron at -47 mV.

  Fe(OH)3+ 3H+ + e- <> Fe+2 + 3H20

   

  All organisms metabolizing Fe, SO-2, methane are strict anaerobes.

  Mn must be depleted before Fe reduction.
• How is sulfate reduced in redox?

  Reduction of sulphate at -221 mV.

  Analogous to denitrification, limited by S04 concentrations.

  SO-2 + IOH+ + 8e- H2S + 4H20

   

  Old metabolism... 2 billion years old.

  S04+2 concentrations are generally low, therefore S04 reduction zone is very small.
• How is methane produced in redox?

  Methanogenesis occurs at -244 mV.

  Once S04 is gone, methanogens take over.

  CH3COOH -9 C02 + CH4

  C02 + 4H+ -4 CH4 + 2H20

  
  

  Limited by concentrations of labile organic matter.

  As CH4 diffuses up, it is consumed by a number of bacteria and oxidized.

  Therefore, CH4 flux to atmosphere depends on the amount produced (source) compared to the amount oxidized (sink).

  Ditto for water column.
• Why is anaerobic respiration important?

  Cycling of carbon, nitrogen, sulfur, Fe, etc., etc, etc...

  Various forms of Mn, As, Se, Te, Cr, V, U, Tc, NP are all biologically reducible.

  Depletes organic carbon.

  Exerts control over metal (radionuclide) speciation.

  Solubilizes some metals, precipitates others.
• what is syntropy?

  Two or more microbes cooperate to degrade a substance neither can degrade alone.
• What are the main determinants of climate?

  Temperature — a function of elevation and latitude

  and precipitation
• What differences can cause varying habitats?

  Rainfall - how soil and environment changes because of precipitation.

  Latitude - how move sun each place gets.
• What are some general facts about soil?

  "skin of the Earth" Soils are less than 1m thick, but are VITAL.

  Extremely heterogeneous (physical, chemical, biological).

  Plant growth complex — driven by abiotic soil architecture and high diversity.
• What are the different zones below the surface of the soil?

  1. Surface soils (unsaturated).
  2. Vadose zone(unsaturated) - oligotrophic, thickness varies.
  3. Saturated zone - shallow aquifers, intermediate aquifers, deep aquifers. Oligotrophic, Water table can rise or fall.
• What is a part of the capillary fringe?

  Capillary fringe - sponge bringing water up and back and forth. This is a "nearly" saturated form.

  Water tables can rise or fall.

  Boundary is called the capillary fringe.

  Several types.

  Non-porous material isolate aquifers.
• What are the different aquifers in the saturated zone?

  Shallow table aquifer - prone to varying daily values.

  Intermediate aquifer - changes on yearly basis. (affected by snow, heavy rainfall).

  Deep aquifer - not really any changes.