Chapter 5: Organisms and Organic Residues

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Chapter 5 Organisms and Organic Residues 51
Important Facts to Know

• The importance of soil organisms and the roles
  they play in maintaining a sound productive
  environment.
• The conditions favoring and potential impacts of
  non-beneficial organisms and their control.
• The nature and composition of soil organic
  matter.
• The role of soil organic matter in improving
  soil chemical physical properties.
• The value and properties of manures, residues,
  domestic waste, and composts.

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Homework Chapter 5

Questions 5, 8, 10, 13, and 15 _at_ 2pts 10
pts Due 14 October 2009
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Kingdoms of Living Organisms

• Animalia rodents, worms, insects
• Plantae - plants
• Fungi molds, mushrooms, mycorrhizae
• Protista algae, protozoa, slime molds
• Monera - bacteria, actinomycetes

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52 Animalia Rodents, Worms Insects

• A. Vertebrates (backbone)
• Burrowing animals Moles, mice, shrews, gophers,
  rabbits, etc. (aeration, structure, fertility,
  plant damage)
• Mix soil with burrowing
• Hasten decomposition
• Create macropores
• Can have major effects on soils plants

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B. Invertebrates (no backbone) 1.
Arthropods Organism Function Beetles
Primary consumer transport and mixing of
organics Ants Primary consumer transport and
mixing of organics movement of B horizon to
surface. Centipedes Predator minor role in soil
formation
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• 1. Arthropods (cont.)
• Organism Function
• Millipedes Saprophageous (feed on dead organic
  matter). Transport and mixing.
• Springtails Primary consumer affect soil
  structure
• Mites Saprophageous very important in
  numbers affect soil structure
• 2. Gastropods Eat decaying vegetation (slugs,
  snails)

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3. Annelids Organism Function Earthworm
(Lumbricidae spp.) most important component of
macrofauna (up to 80 of biomass). - Very
important in soil structure 1 order
breakdown -Sensitive to pH and moisture -Casts
are enriched in N and P major role in mixing
organic matter -2 million/ha in beech forest,
10 million/ha in pasture. None to few in acid
soils.
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• Lumbricidae terrestris
• Originated in Europe
• Uncommon in North America before European
  settlement.
• Major effect upon forest floor and soil organic
  matter in North America, especially in riparian
  areas. Now considered a major problem in many
  ways, including native plants.

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4. Nematodes Important as population regulators
and nutrient concentrators -Nearly microscopic
roundworms -Common in mull and grassland soils
some in forest soils -Can be parasites (roots)
or predators (on bacteria, fungi) -Fumigation
often improves tree growth may be due to
reduction of parasitic nematodes
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53 Plantae (Plants)

• Roots 30-40 of plant mass
• Root hairs (single cell)
• Rhizosphere zone within 1 mm chemically
  changed, high bacterial concentrations
• Rhizosphere organisms decompose soil organic
  matter and mobilize nutrients from it

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54 Fungi Molds, Mushrooms, Mycorrhizae

• Many ways to classify
• One useful way is into these two major groups
  based on how they get energy
• Autotrophic Use sunlight inorganic chemical
  reactions for energy
• Heterotrophic Use organic compounds for energy

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Molds, Mushrooms, Yeast, Rusts

• Heterotrophic
• Tolerate low pH (most important in decomposition
  in acid forest soils because bacteria are
  acid-sensitive and do not perform well in acid
  systems)
• Decomposers of OM
• Mycorrhizae fungus root
• - Symbiotic with plant roots
• - essential to growth in many cases (e.g.,
  pines)
• - aid in taking up water and nutrients
  (especially P), and they get carbohydrates in
  return

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• Two basic kinds of Mycorrhizae
• Ectomycorrrhizae
• Penetrate only outer cell layers of root and only
  intercellular spaces (Fig 5.4)
• Form a sheath/mantle of mycelium on fine roots
  called Hartig Net
• Common in trees (pines, spruces, larches, D. fir,
  oak, birches, beeches, hickory, cottonwood,
  eucalyptus, aspen)

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• 2. Endomycorrhizae
• Penetrate host cells and change root morphology
  (monopodal, bifurcate, corroloid
• Vesicular arbuscular mycorrhizae (form vesicles
  inside host cells - storage)
• Occur in many plants including some trees

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55 Protista Algae, Protozoa Slime Molds

• Protozoa
• Consume decomposing organic matter, bacteria,
  and fungi
• 1-celled organisms, motile (cilia or flagellum)
• Cause of several human diseases (malaria,
  sleeping sickness, dysentery)

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• Algae
• Carrry on photosynthesis (autotrophic)
• Not decomposers
• Green, blue-green (the latter now called
  cyanobacteria) fix N

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56 Monera Bacteria Actinomycetes

• Bacteria
• Single-celled rod or spherical, 1-2 µm
• 1 tsp 100,000,000 bacteria
• Three subdivisions based on how they handle
  oxygen
• Anaerobes Live only in the absence of O2
• Facultative Can live in either the presence or
  absence of O2
• Aerobes Live only in the presence of O2

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• Two major subdivisions based on how they get
  energy
• Hetertrophs Live on dead organic matter
• Autotrophs energy from sunlight or chemical
  reactions
• Photoautotrophs use sunlight
• Chemoautotrophs use inorganic chemical
  reactions

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Some Important Chemoautotrophs
Nitrifying bacteria One of the most important
autorophic bacteria are nitrifying bacteria, who
convert ammonium (NH4) to nitrite (NO2-) and
nitrate (NO3-) 2NH4 3O2 --------gt 2NO2-
4H 2H2O Nitrosomonas 2NO2- O2 -------gt
2NO3- Nitrobacter
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Very pH-sensitive (don't live below pH 5) Since
they produce acid, they are self-limiting.
However, nitrification has been observed in very
acidic forest soils. Nitrification in these
cases may be accomplished by heterotrophic
nitrifiers or in microsites
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Sulfur oxidizing bacteria (not in chapter
5) Another important chemoautotroph is the Genus
Thiobacillus most important of chemoautotrophic
mineral oxidizers (elemental sulfur and sulfide
minerals). For elemental S 2S 3O2 2H2O
-------gt 4H 2SO42- Thiobacillus
thiooxidans
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One important reaction carried out by these
bacteria is the oxidation of pyrite, FeS2, which
occurs commonly in mine spoils by Thiobacillus
thiooxidans and Thiobaccillus ferroxidans 4FeS2
1502 2H2O ? 2Fe2(SO4)3 4H 2SO42-
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• Some Important Heterotrophs
• 1. Decomposers
• 2. Nitrogen-fixing bacteria
• Decomposing bacteria
• Both aerobes and anaerobes
• Very important for nutrient cycling convert
  nutrients from solid phase to ions which go into
  soil solution

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• Nitrogen fixers
• Convert N2 gas in the atmosphere to ammonium
  (NH4) in the nodules of roots in certain plants
• Very important source of N for soils and
  vegetation, especially in unpolluted areas
  soils have no mineral N source!
• The atmosphere is 78 N2 gas but plants cannot
  utilize it because of the strong triple bond.
• Nitrogen fixers take energy from host plants and
  convert this N to usable form using nitrogenase
  enzyme.

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• Two subdivisions of nitrogen fixers
• Non-symbiotic N2 fixers Exist as free bacteria,
  but get energy from nearby organisms (plant
  rhizosphere, lichens)
• Symbiotic N2 fixers live in plant roots, get
  energy from plant carbohydrates (heterotrophic)

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• Symbiotic N fixers include both bacteria and
  actinomycetes
• Rhizobium bacteria
• Associated with the root nodules of legumes
• (e.g., Lupine, clover, alfalfa, soybean).
• Can fix up to 300 kg ha-1 yr-1 (atmospheric
  deposition 1-25).

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• Frankia spp. actinomycetes
• Various tree and shrub species (Alnus, Myrica,
  Elaeagnus, Ceanothus, Cuasarina)
• These are more important than legumes in
  forests. Can also fix up to 300 kg ha-1 yr-1
  (atmospheric dep 1-25).

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Symbiotic N fixers Frankia actinomycetes Excessiv
e N fixation has been shown to cause
nitrification, nitric acid formation, nitrate
leaching, and soil acidification in red alder
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• Free living N-fixers
• Do not need a host plant
• Usually fix much less than symbiotic fixers
• Aerobes Azotobacter, A. beijerinckia, (hetero)
• Anaerobes Clostridium, (most common)
• Blue-gree algae (Cyanobacteria).
• Often associated with plant roots present in
  cryptogamic/biotic crusts.
• Believed to be first fixers 2-3 billion years
  ago.

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• Actinomycetes
• 5-20 µm dia, 0.1 - 1 m long (filaments, but more
  similar to bacteria)
• Morphologically transitional from bacteria to
  filamentous fungi
• Unicellular, slender branced mycelium
• Numerically second only to bacteria
• Aerobic, like pH gt 5
• Active in decay of cellulose and other organics
  (hetero)
• Frankia genus active in nitrogen fixation (as
  noted above)
• Some produce antibiotics (exudates which kill
  bacteria)

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57 Soil Viruses and Viroids

• Non-cellular
• Non-living nucleic acids with a coating
• Cause many plant diseases often spread by
  carriers control is to control the carriers
• Prion nucleic acids with no coat
• Viroid no coat around RNA
• Virus coat
• Soil can function as a repository chronic
  wasting (mad cow disease).

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58 Conditions for Microbial Activity

• Moisture near FMC
• pH near 7 for bacteria do not do well below pH
  5
• Temp biological activity increases 2x as temp
  goes from 10 to 20 C
• Exceptions
• Psychrophiles can grow at lt5 C, opt at 15 C
• Mesophiles slight growth at 0 C, little growth
  gt40 C, opt at 25-37 C
• Thermophiles tolerate 45-75 C, opt at 55-65
  (composters)

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• Encouraging good microbes
• Inoculation
• Lime
• Minimize sterilization
• Maintain SOM
• Avoid contamination
• Avoid stress (drought, temp, etc)

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• Controlling bad microbes
• Start with clean plants
• Sanitation
• Minimize mechanical damage
• Control water Not too humid
• Control soil acidity
• Control infestations quickly (spray)

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59 Composition of Organic Matter (Soil Organic
Matter SOM)

• 40-50 C, then H, O, N, P,.
• C-chains
• Humic substances colloidal, amorphous,
  polymeric, dark-colored materials end products
  of extensive decomposition
• Functional breakdowns of humus
• Humic acid soluble in NaOH, but not in HCl
• Fulvic acid soluble in both
• Humin insoluble in both
• SOM is very complex, from simple sugars to
  complex humic substances.

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510 Decomposition of SOM Activation energy
what it takes to push the reaction over the edge
(fire is example)
Energy needed to sustain the reaction
Energy
Reaction
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Enzymes lower activiation energy by acting as
catalysts (substances which activate the
reaction but are consumed by it) Insight on p.
145, Table 5-4 are examples of enzymes Products
of decomposition nutrients are converted from
the organic form (not useable by plants) to
inorganic forms (available to plants and
microbes) CO2, NH4, H2PO4-, SO42-, Ca2, K,
Mg2, Na, H2O
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Factors affecting decomposition

• Moisture too dry (aridisols) or too moist
  (histosols)
• Temperature
• Nitrogen Carbon to nitrogen ratio (CN ratio)
  a fundamental property of soils that relates to
  nitrogen status

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Both litterfall and decomposition increase with
mean annual temperature however, decomposition
increases more rapidly and thus O horizon mass
decreases
Decomposition
O Horizon mass
Litterfall
Mean Annual Temp
Mean Annual Temp
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Cold ecosystem Warm Ecosystem
CO2
Litterfall
CO2
Litterfall
O Horizon mass
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• Other factors affecting the accumulation of soil
  organic matter
• Texture very important for SOM accumulation
  surfaces adsorb (especially allophane and
  sesquioxides)
• pH too low inhibits decomp
• Disturbance ploughing is the best example (lost
  40 SOM in Great Plains since agriculture) - this
  allowed early settlers to grow crops w/o
  fertilizer (that is over now) and create dust
  bowls.

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511 Effects of Soil Organic Matter

• Improve physical and chemical properties
• Aeration, WHC, structure, drainage
• Ion exchange, chelation
• Source of available nutrients
• Allelopathy

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• CN Ratio of Organic Organic Matter
• In order for soil microbes to decompose most
  litter types, they must initially incorporate N
  from the soil.
• Thus, inputs of high CN ratio litter can cause
  N deficiency to plants unless accompanied by
  fertilization.
• As C is lost at CO2 gas, the C/N ratio of the
  litter decreases to a value ranging of about 201
  N is released from decomposing litter
• (Figure 5-9)

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CN Ratio of Organic Organic Matter Compare the
CN ratio of decomposers (microbes) with that of
the litter they must decompose
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• Nitrogen Cycling in Soil
• CN ratios of litter substrate is often much
  greater than in microbe bodies
• Therefore, microbes keep the N, release the C as
  CO2, thereby reducing the CN ratio

Carbon
CO2
Nitrogen
Microbes CN 12
Organic Substrate CN 12 to 200
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• Nitrogen Cycling in Soil
• In order to consume very high CN ratio material
  (such as wood), microbes may need to import
  ammonium (NH4) from the soil
• This is called N immobilization
• It steals available N from plants!

Plants
Carbon
CO2
X
Nutrients
Immobilization
Microbes CN 12
Organic Substrate CN 200
NH4
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• Nitrogen Cycling in Soil
• Once microbes have satisfied their N demands,
  they release N as ammonium (NH4) during
  decomposition as they continue to get energy from
  the organic C
• This is called N mineralization, and it provides
  available N to plants

Plants
Carbon
CO2
Nutrients
Mineralization
Microbes CN 12
Organic Substrate CN 12 to 200
NH4
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CN Ratio of Organic Organic Matter
As a rule of thumb At CN gt201, NH4 is
immobilized At CN lt 201, NH4 is mineralized
CN lt 201
Organic matter plus microbe N
NH4
CN gt201
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512 Organic wastes

• Animal manure
• Municipal sludge application to land instead
  of dumping in water
• Composting