2. Review of Soil Biology

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2. Review of Soil Biology

• Textbook chapter 5

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Importance of Microbial Processes in Soil, the
Vadose Zone, and Water

• Nutrient cycling.
• e.g. N, C, and S cycles.
• Degradation of organic pollutants.
• Control oxygen content
• Control redox potential when oxygen is limiting.

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Microbial Energetics

• Energy is required for microbes.
• For non photosynthetic microbes, energy is
  provided by oxidation of compounds of C and other
  elements.

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Microbial Energetics cont.

• Enzymes catalyze energy releasing reactions.
• Catalysis allows the energy producing reactions
  to occur at low temperature.
• Involves oxidation and reduction.
• See your intro chemistry textbook.

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Microbial Energetics cont.

• Oxidation of C compounds by O2
• C6H12O6 9O2 ? 6CO2 6H2O
• Glucose
• O2 is the electron acceptor.
• Gains e- and reduced from 0 to - 2 oxidation
  state
• C is the electron donor.
• Loses e- and oxidized from 0 to 4 oxidation
  state
• Energy yield
• ?GO - 2870 kJ mol-1 (not ?G as in textbook)

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Mode of Nutrition

• Heterotrophs
• Need a source of organic C for energy.
• Carbon compounds are the electron donors.
• Autotrophs
• Use non C compounds or the sun as a source of
  energy.
• For chemoautotrophs inorganic compounds are
  electron donors.

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Aerobes vs.. Anaerobes

• Aerobes
• Use O2 as the electron acceptors in the reaction
  that produces energy.
• Anaerobes
• Use compounds other than O2 as electron
  acceptors.
• e.g. NO3-, Fe(III), and SO42-.

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Examples Microbial Nutrition

• Aerobic heterotrophic
• Aerobic transfer of electrons from reduced C to
  oxygen.
• e.g. Oxidation of benzene (a component of fossil
  fuels) in the presence of oxygen.
• In benzene the oxidation state of C -1.
• In CO2 the oxidation state of C 4.

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Examples Microbial Nutrition

• Anaerobic (heterotrophic)
• Oxidation using an electron acceptor other than
  O2.
• e.g. Oxidation of glucose in the presence of
  nitrate by Pseudomonas denitrificans
• 5 C6H12O6 24 KNO3 ? 30 CO2 18 H2O
  24 KOH 12 N2
• C oxidized to 4 and nitrate reduced from 5 to
  0.

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Examples Microbial Nutrition

• Autotrophs
• Chemoautotroph
• Use reduced forms other than C compounds for
  energy source.
• e.g. Oxidation of S by thiobacillus thiooxidans.
• S 2O2 H2O ? H2SO4
• S oxidized from 0 to 6
• Photoautotrophs
• Photosynthetic organisms

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In class exercise

• . What is the oxidation number of C in glucose,
  in methane (CH4), and in octane (C8H18)? Want is
  the oxidation number of S in elemental sulfur in
  sulfuric acid.

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Answers

• Methane and octane
• H is 1 so C is - 4 in methane
• On average C is -2.25 in octane.
• The oxidation state of elements is O
• H2SO4
• O is -2 H is 1 S is 6.

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Types and Abundance of Microbes

• Bacteria, actinomycetes, and fungi are the three
  major groups.
• Very abundant in soils.
• Less in vadose zone and in ground and surface
  waters.

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Abundance of microbes in surface soil.
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Some Soil Bacteria

• Pseudomonas
• 10-20 of culturable bacteria.
• Mostly heterotrophs.
• Mostly aerobic.
• Many different degradative enzymatic systems.
• Capable of degrading many organic compounds.
• Important in cleaning up soils of pesticides,
  oily pollutants, etc.

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Some Soil Bacteria

• Bacillus
• 10 bacteria.
• Heterotrophic.
• Diverse.

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Ordinary Bacteria, Fig. 4-1
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Some Soil Bacteria

• Actinomycetes
• 5 20 of soil microbes.
• 90 streptomycetes.
• Actinomycetes usually considered separately from
  ordinary bacteria.
• Can metabolize a wide variety of organic
  compounds.
• e.g. cyanide (CN-1) and phenol.

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Soil Fungi

• Heterotrophic
• Mostly aerobic
• Yeasts are anaerobic fungi.
• Fermenting organisms.
• Filamentous molds are very important for the
  degradation of organic compounds.
• Diverse enzymes.

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Soil Fungi (cont.)

• Generally tolerant of low pH.
• Abundant in soils.
• More mass than bacteria or actinomycetes.
• Less numbers.

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Actinomycetes and Fungi, Fig. 4-1
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In Class Exercise

• Write balanced equations for aerobic oxidation
  of methanol (CH3OH), methane (CH4), by bacteria.
  
• Which requires more O2 and which yields more
  energy per mole of C?

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Answer

• CH3OH 3/2O2 ? CO2 2H2O
• C has an oxidation number of 3-
• CH4 2O2 ? CO2 2H2O
• C has an oxidation number of 4-

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Effect of Low Oxygen in High Moisture Soils

• Were moisture is high, O2 is excluded.
• Aerobes die or become dormant.
• Facultative and obligate anaerobes grow in wet
  soil.
• Facultative microbes can function both with and
  without O2.
• Obligate anaerobes function only without O2.

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Lack of Oxygen and Redox Potential

• Standard electrode potentials, EH, indicates the
  level of oxidation or reduction.
• When oxygen is present at neutral pH EH 800
  mV.
• After O2 is used up reduction of NO2- to N2 or
  N2O (nitrous oxide) occurs EH 740mV
• Facultative anaerobes.
• Reduction of SO42- for S2-, EH -220 mV.
• Obligate anaerobes.

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Examples of Anerobes

• Electron acceptors other than O2 are reduced.
• e.g. metabolism of Desulfovibrio
• H3CHOHCOOH SO42- ? 2CH3COOH HS-
• lactic acid acetic acid H2CO3
  HCO3-
• Lower energy yield compared to aerobic reactions.

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At very low EH C in carbohydrates can both be
oxidized and reduced

• Carbohydrates can be metabolized to methane and
  CO2, EH -300 mV.
• C6H12O6 ? 3CO2 3CH4
• glucose methane
• Reaction in anaerobic digesters used in treatment
  of sewage sludge and methane digesters.
• Obligate anaerobes.
• C is both oxidized and reduced

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Effect of soil pH

• Soil pH
• Most microbes grow best at pH 6-8.
• Fungi can do quite well in acid soils (4-6)
• More competitive at acid pH values.
• Actinomycetes can do well and pH 8-9
• More competitive at high pH
• Some specialized organisms are adapted to more
  extreme pH values.
• e.g. Thiobacillus thiooxidans
  (pH optimum 2-3).

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pH and EH Preference of Microbes
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Ability of soil microbes to respond to changes in
conditions

• Diversity to exploit conditions as they vary with
  time.
• Diversity to exploit the various niches in the
  soil.
• Most organism not active most of the time.
• Many very specialized organism.
• Most soil organisms cannot be grown in culture
  media.
• Soil is a very robust biochemical system.

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Summary

• Microbes can catalyze the degradation of organic
  compounds.
• Three type of organisms.
• Bacteria
• Actinomycetes
• Fungi
• Microbe can use different electron acceptors.

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• Microbes vary in tolerance to different pH,
  temperature, and soil moisture.
• Soils are a robust biochemical systems.

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Problem for next lecture

• If a soil contains 1.0 x 108 bacteria per gram.
  How many bacteria are in a cubic meter of soil if
  the soil bulk density is 1.3 g cm-3.