7270 Advanced Soil Ecology Soil Environment

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7270 Advanced Soil EcologySoil Environment

• Dr. Mario Tenuta
• Department of Soil Science
• x7827
• tenutam_at_cc.umanitoba.ca

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Modern versus Old Soil Ecology

• Soil ecology and biology in general have been
  minor components of Soil Science Departments and
  in most cases journals
• The science of soil has concentrated on
• Pedogenesis
• Fertility
• Water and physical properties
• Soil limitations
• Soil biology was usually incorporated into soil
  fertility
• Result of tie to soil fertility
• Chemical approach
• Quest to identify amounts of nutrients
• Treat soil as a black box

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What is a Black Box?

• Emphasize the inputs, outputs and change in
  storage of energy, elements and compounds in soil
  studies

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Where Do Soil Ecologists Historically Fit?

• Earliest Universities to teach soil microbiology
  were agricultural schools or faculties
• Microbiology departments evolved but usually
  studied invitro systems
• Biology departments studied natural systems and
  little understanding between researchers of
  natural and agricultural systems
• Soil biologists had agricultural backgrounds and
  worked in agricultural systems

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Where Do Soil Ecologists Fit Now?

• Times have changed
• Realization of fundamental similarities between
  agricultural and natural systems
• Fewer students in agricultural faculties but
  still need for soil microbiologists thus graduate
  students coming from Biology backgrounds
• Environmental issues and complexity of nature
  require need for Soil Ecologists in many
  different departments

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Examples of Where Soil Ecologists Fit in
Universities

• Biology departments with strength in Ecology
• Distribution of microbial and plant communities
• Ecology of soil animals
• Geography and natural resource departments
• Climate change studies effect of microbial
  processes on greenhouse gases
• Microbiology Departments
• Molecular and functional diversity
• Engineering
• Bioremediation, waste disposal/sanitation
• Applied Departments
• Soil Science
• Forestry
• Plant Pathology
• Fertility, pathology and pests, root morphology,
  animal pathogens
• Impact of anthropogenic activities

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What is in a Name?

• Soil Microbiology
• Often study of biochemical and molecular
  processes of individual or consortia of
  microorganisms
• Soil Biology
• Often the study of non-microscopic organisms
• Soil Ecology
• Where many types of organisms (microscopic and
  non-microscopic) are studied simultaneously and
  emphasis placed on interactions

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Factors Affecting Soil Organisms

• Chemical
• Mineral nutrients
• Ionic composition
• Atmospheric composition
• pH
• Growth factors
• Carbon and energy sources
• Oxidation-reduction potential

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Factors Affecting Soil Organisms

• Physical
• Available water
• Temperature
• Pressure
• Electromagnetic radiation
• Surfaces

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Factors Affecting Soil Organisms

• Biologic
• Spatial relationships
• Genetics of microorganisms
• Interactions between microorganisms (competition,
  mutualism, antagonism)

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Regosolic Soil
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Cryosolic Soil
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Black Chernozem
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Grey Chernozem
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Brown Chernozem
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Solonizic Soil
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Gleysol
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Podzol
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Anthropogenic Soil - Landfills
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Harsh Soils Serpentine Soil Gros Morne
Newfoundland
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Anthropogenic ally Contaminated Soil
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Factors of Soil Formation
Soil development f (climate, relief, organisms,
parent material, time)
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Components of Soil

• Solids
• mineral particles of various sizes and shapes
• organic matter in various stages of decomposition
• living organisms and plant roots
• Liquids
• Liquids
• Dissolved compounds
• Gases
• Space other than solids or liquids

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Structural Aspects Soil Pore Space

• Habitat of most soil microorganisms
• Some live in pore spaces of plant residue
• Some like earthworms just ingest soil
• Calculated as
• soil volume - bulk density / 2.65 g cm-3

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Size of Soil Organisms
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Pore Size Exclusion or Habitable Pore Size Theory

• Soil organisms are restricted to pores greater
  than their diameter

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Soil Temperature

• Affects physiological reaction rates
• Affects chemical reaction rates
• Redox potential
• Diffusion
• Brownian movement
• Viscosity
• Surface tension
• Water structure
• Optimal temperature differs with soil organisms
• Psychrophiles (high latitudes and altitudes)
• Mesophiles (most arable soil)
• Thermophiles (hotsprings, composts)
• Extreme thermophiles
• Heat stress
• Denaturing of enzymes,
• Cold stress
• Decrease in fluidity of cellular membranes
• Ice nucleation

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Why an Optimum Temperature?
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Selection to Temperature
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Soil Temperature Varies Temporally and Spatially

• At soil surface follows diurnal pattern of
  atmosphere
• Soil with higher moisture are cooler
• Decreases with depth in late spring and summer,
  increases with depth in the fall
• At soil surface can reach 50oC

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• Arrhenius developed an equation describing the
  rate of a reaction as a function of temperature
  and it bears his name
• kAe(-Ea/RT)
• k rate of reaction s-1
• A constant s-1
• Ea Activation energy (J mol-1)
• R universal gas constant (8.314 J mol-1 K-1)
• T temperature in K

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Example
Temperature dependence of C2H4 removal in batch
incubations of biofilter soil. The insert shows
an Arrhenius plot with linear regression of data
below the optimum temperature.
Applied and Environmental Microbiology, 2000,
663878-3882
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Q10

• A useful characterization of activity as a
  function of temperature is the Q10 value
  (Quotient value 10 C range)
• It is described the relative rate of a reaction
  over a 10 C range
• Q10  (k(T10) k(T) )
• Q10 lt1 (inhibition of reaction by temperature)
• Q10 1 (no effect of temperature)
• Q10 gt1 (temperature increases reaction)

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Factors Controlling Minimum Temperature for
Microbial Activity

• A) freezing of cytoplasmic membrane
• unsaturated fatty acids increase fluidity and
  drops minimum temperature
• thermophiles (10) mesophiles (37)
  psychrophile (52)
• B) Ability of enzymes to catalyze reactions at
  low temperature
• produce more enzymes to compensate for lower
  activity
• protein structure more flexible due to
• weaker non-covalent interactions between
  polypeptide backbone and between side-chains of
  amino acids
• weaker hydrophobic bonding in interior and
  stronger hydrophilic interactions at exterior
• more glycine residues
• more surface loops that are hydrophilic
• reduced hydrophobic links between subunits
• fewer H bonds, aromatic interactions and ion
  pairs
• accumulate solutes in cytoplasm to prevent drying
  and crystal formation
• C) Produce extracellular mucilage

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Factors Controlling Minimum Temperature for
Microbial Activity

• D) Functioning ribosomes at low temperature
• E) Increasing concentration of solutes in cells
• Do not affect cellular function but increase
  water potential and depress freezing point
• Ex. trehalose, proline, K
• F) Increasing concentration of ice nucleating
  compounds

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Soil Water

• Essential for the activity and growth
• Physiologic processes require water
• Require water to
• Move in
• Exchange gases
• Exchange solutes
• Expel wastes
• Obtain nutrients
• Available water can be in
• Occupying pores
• Films around particles and organisms
• Water flows from area of high potential to low
  potential
• Water potential is given as MPa (mega Pascal)

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What is Water Potential

• Osmotic potential
• Attraction of ions in solution for water
  molecules
• Dissolved compounds reducing the density or
  concentration of water molecules
• Matric potential
• Adsorption of water to charged soil particles
• Pulled by capillary action in very fine pores
• Affected by soil texture, structure, organic
  matter, and bulk density

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Osmotic potential of soil solution for 17 soils
from the western US at a matric potential of 1.5
MPa. (from Magistad and Reitemeier 1943)
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Water Potential - Matric Potential

• Matric potential mainly controls microbial
  activity
• Determines diameter of pores filled with water
• Thickness of water films around particles and
  organisms
• Applies tension preventing microbial uptake

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Microbial tolerance to matric-controlled water
stress. (From Harris 1981)
Note film thickness of 3 water molecules
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Soil Atmosphere

• Different from above ground atmosphere
• Some gases higher in composition produced
• CO2
• C2H4
• N2O
• Some gases lower in composition consumed
• O2
• CH4

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What Determines Soil Gas Composition?

• Production
• Consumption
• Transfer between soil and above-ground atmosphere
• Mass flow
• positive or negative atmospheric pressure (wind)
• displacement by / replacement of water
• Diffusion
• dependent upon concentration gradient between
  atmosphere and soil
• ability of soil to transfer gas diffusivity

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Soil Aeration

• Measure of O2 status of soil
• Soil is a sink for O2
• Aeration is good if rapid exchange of gases
  between atmosphere and soil
• Aeration is poor when not
• Important O2 needed for respiration
• Obligate aerobes need O2
• Faculative aerobes can use O2 and other compounds
• Obligate anaerobes find O2 lethal

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Oxygen Concentration
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Redox Potential

• Soil aeration commonly determined as redox
  (reduction oxidation) potential
• State of soil to accept or donate electrons
• As e- lost (e.g. Fe2 to Fe3) potential becomes
  positive (oxidized)
• As e- gained (e.g. Fe3 to Fe2) potential
  becomes negative (reduced)
• potential (oxidized environment, O2 present)
• - potential (reduced environment, O2 lacking)

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Redox Potential
Redox potential determines biochemical pathways
by which microorganisms obtain energy
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Anaerobic Microsite Theory

• Observations
• facultative and anaerobic bacteria active in
  aerobic soil ?
• Anaerobic activity increases with
• Soil aggregation
• Moisture
• redox potential in centre of large aggregates

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Soil pH

• Soil organisms have optimal soil pH range
• Nutrient acquisition
• Extracellular enzyme activity
• Regulate cytoplasmic pH from that of soil
  solution
• Fungi are acid tolerant (pH 4 to 6.5)
• Bacteria prefer neutral conditions (6.0 to 7.5)
• Organisms have ability to alter soil pH
• Ammonium oxidizing bacteria acidify soil by
  producing NO3- from NH4

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Soil Structure and Aggregate Formation

• Groups of soil particles adhere to produce soil
  aggregates
• Aggregates range in size from 0.5 to 5 mm in
  diameter
• Largest being clusters of aggregates producing
  macroaggregates greater than 5 mm in diameter
• Aggregates determine structure, porosity,
  aeration, water retension, pore space and sizes

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Soil Organisms and Products of Their Activity
Create Soil Structure

• Soil particles and organic matter are negatively
  charged
• Compounds produced by microorganisms are
  attracted to soil particles
• Enzymes
• Polysaccharides
• Wastes
• Fragments
• Bacteria and fungi negatively charged should be
  repelled from soil surfaces
• Can bind to soil particles and organic matter
  through intermediates
• Divalent cations
• Adsorbed organic compounds

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The Hierarchical Model of Soil Structure
Formation