Soil Organisms

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Soil Organisms
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What creatures live in soil?
22 species
Harvester Ant Colony
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Fauna
Macro
Micro
Mammals, reptiles, insects, earthworms
Nematodes, Protozoa, Rotifers
Flora
20,000 species
Plant roots, algae, fungi, actinomycetes
(filamentous bacteria), bacteria
unicellular
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Macrofauna Earthworms
1,000,000 per acre
five pairs of hearts
Mostly intestine
22 ft. long (Afr. and Aus.)

• Earthworm cast
• Casts earthworms wastes
• Eat soil organics 2-30 times of their own wt.

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Earthworms

• Abundance of earthworms
• 10-1,000/m3
• 3,000 species
• Benefits of earthworms
• soil fertility by producing cast
• aeration drainage
• size stability of soil aggregates

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Soil Fungi
Yeasts, molds, mushrooms
10 - 100 billion/m2 Cell with a nuclear membrane
and cell wall Most versatile most active in
acid forest soils
Tolerate extremes in pH (bacteria do not)

• Mycorrhizae symbiosis
• Association between fungi plant root
• Increased SA (up to 10 times)
• Increased nutrient uptake,
• especially P

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Mycorrhizae Fungi

1. Ions in solution
2. Movement from solution to root (diffusion)

Phosphorous granule
Fungal hyphae
Root hair
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Symbiosis

• Fungi provide nutrients
• Plant root provides carbon
• Ectomycorrhiza Root surfaces and cortex in
  forest trees
• Endomycorrhiza Penetrate root cell walls
• agronomic crops-
• corn, cotton, wheat, rice

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Soil Bacteria

• 10-100 trillion/m2
• Single-celled organisms
• Rapid reproduction
• Small (lt5 µm)
• Mostly heterotrophic

Autotrophic Bacteria Impact the availability of
soil nutrients (N,S)
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Quantification of Soil Organisms
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Quantification of Soil Organisms
Three Criteria

• Numbers of organisms
• Extremely numerous
• 1,000,000-1,000,000,000 /g soil
• 10,000 species /g soil
• Biomass
• 1-8 of total soil organic matter
• Metabolic activity
• Respiration CO2
• Proportional to biomass

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Soil Organisms in Surface Soils

• Organisms /g soil Biomass (g/m2)
• Microflora
• Bacteria 108 -109 40-500
• Actinomycetes 107 -108 40-500
• Fungi 105 -106 100-1,500
• Algae 104 -105 1-50
• Fauna
• Protozoa 104 -105 2-20
• Nematodes 10 -102 1-15
• Mites 1 -10 1-2
• Earthworms 1 -10 10-150

Note those in White
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Basic Classification of Organisms
Food Oxygen Energy Source
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Based on food live or dead

• Herbivores
• Eat live plants
• Insects, mammals, reptiles

• Detritivores
• Eat dead tissues
• Fungi, bacteria

• Predators
• Eat other animals
• Insects, mammals, reptiles

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Based on O2 demand

• Aerobic
• Active in O2 rich environment
• Use free oxygen for metabolism
• Anaerobic
• Active in O2 poor environment
• Use combined oxygen (NO3- , SO4-2)

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Based on energy C source

• Autotrophic (CO2)
• Solar energy (photoautotrophs)
• Chemical reaction w/inorganic elements
• N, S, Fe (chemoautotrophs)

• Heterotrophic
• Energy from breakdown of organic matter Most
  Numerous

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Organisms are Major Determinants of Water
Quality and the Impact or Availability of Water
Pollutants
Metals (Hg, Pb, As) Nutrients (N, P) Organic
Chemicals (PCBs, Dioxins)
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The Earliest Organisms
Autotrophic produce complex organic compounds
from simple inorganic molecules and an
external source of energy.
Organic Carbon-containing
Chemoautotrophs, Cyanobacteria, Plants
3.5 bya
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Autotrophs Plants, Algae, Cyanobacteria
Produce complex organic compounds from carbon
dioxide using energy from light.
energy
light
6CO2 6H2O C6H12O6 6O2
complex organic compound
simple inorganic molecule
Primary producers base of the food chain
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Heterotrophs
Derive energy from consumption of complex
organic compounds produced by autotrophs
Autotrophs store energy from the sun in carbon
compounds (C6H12O6) Heterotrophs consume these
complex carbon compounds for energy
autotrophs
Heterotrophs
carbon compounds (C6H12O6)
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Organisms
Heterotrophs use carbon compounds for energy
- consumers
Heterotrophs
Anaerobic live in low-oxygen environments Aerobi
c live in high oxygen environments
Aerobic heterotrophs Anaerobic heterotrophs
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Aerobic Heterotrophs and Anaerobic Heterotrophs
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Aerobic Heterotrophs
Live in high-oxygen environments Consume organic
compounds for energy
Obtain the energy stored in complex
organic compounds by combining them with oxygen
C6H12O6 Oxygen energy
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Aerobic Respiration
C6H12O6 6O2 ? 6CO2 6H2O
energy
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The energy is obtained by exchanging electrons
during chemical reactions.
C6H12O6 6O2 ? 6CO2 6H2O
2880 kJ of energy is produced
Aerobic respiration is very efficient, yielding
high amounts of energy
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Anaerobic Heterotrophic Organisms
Live in low-oxygen environments Consume organic
compounds for energy
Can use energy stored in complex carbon
compounds in the absence of free oxygen
The energy is obtained by exchanging electrons
with elements other than oxygen.
Nitrogen (NO3) Sulfur (SO4) Iron (Fe3)
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Aerobic Respiration
C6H12O6 6O2 ? 6CO2 6H2O
Anaerobic respiration
C6H12O6 3NO3- 3H2O 6HCO3- 3NH4
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Anaerobic respiration is less efficient and
produces less energy.
C6H12O6 6O2 ? 6CO2 6H2O
2880 kJ
C6H12O6 3NO3- 3H2O 6HCO3- 3NH4
1796 kJ
C6H12O6 3SO42- 3H 6HCO3- 3HS-
453 kJ
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The oxygen status of soil/water determines the
type of organisms aerobic or anaerobic
Low-oxygen
High-oxygen
Oxygen status impacts availability of nutrients
as well As the availability and toxicity of some
pollutants
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Example Eutrophication
Nutrient addition increases primary productivity
(algae)
Sunlight is limited at greater depth
Photoautotrophs die and become food for aerobic
heterotrophs
Aerobic autotrophs consume oxygen Oxygen content
in water is reduced
bacteria
If oxygen is reduced sufficiently, aerobic
microbes cannot survive, and anaerobic microbes
take over
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Respiration and Still Ponds
O2
Aerobic heterotrophs consume oxygen
Heterotrophic Organisms
NO3-
Anaerobic heterotrophs Use nitrate instead of O2
oxygen
SO4-2
Anaerobic heterotrophs Use sulfate instead of O2
SO4-2 HS-
C6H12O6 3SO42- 3H 6HCO3- 3HS-
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Organisms and Nutrients
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Nitrogen
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Nitrogen and Soil
The most limiting essential element in the
environment
Surface soil range 0.02 to 0.5
0.15 is representative
1 hectare 3.3 Mg
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Biological/Plant Nitrogen
Component of living systems
Amino acids Proteins Enzymes Nucleic acids
(DNA) Chlorophyll
Strongly limiting in the Environment
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Deficiency
Chlorosis pale, yellow-green appearance
primarily in older tissues.
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Excess
Enhanced vegetative growth lodging Over
production of foliage high in N Delayed
maturity Degraded fruit quality
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N Distribution/Cycling
Atmosphere Soil / soil O.M. Plants, animals
N2, NO, N2O
NH4, NO3-, R NH2
Proteins, amino acids
Organic Nitrogen (plant tissue, Soil Organic
Matter) R NH2
During organic decomposition, R NH2 is usually
broken down to NH4
NH4 is converted to NO3- by soil microorganisms
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Forms mineral and organic
Organic plant/tissue N R-NH2 Mineral soil N
NH4, NO3-
Cycling in the Environment
Mineralization Decomposition of organic forms
releasing nitrogen into the soil,
generally as NH4 Immobilization Plant uptake
of mineral nitrogen, removing it from the soil
and incorporating into plant tissue.
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Ammonium and Nitrate
Mineralization
NH4
R NH2
organic mineral
Immobilization
R NH2
NH4 or
NO3-
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Cycling of Nitrogen
R-NH2 is organically bound form of nitrogen
X
R-NH2
NH4 is exchangeable, NO3- is not
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Atmospheric Nitrogen Fixation
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Forms of Nitrogen
R-NH2 is organically bound form of nitrogen
X
R-NH2
NH4 is exchangeable, NO3- is not
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Symbiotic Biological Nitrogen Fixation
Symbiosis between plant roots and rhizobium
bacteria
Rhizobium
N2
NH4
Nodules are packed with Rhizobium
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Nitrogen and Legumes
Residue from legume crops is usually high in N
when compared with residue from other crops and
can be a major source of N for crops that follow
legumes in rotation. Most of the N contained in
crop residue is not available to plants until
microbes decompose the plant material.
N Contributions
alfalfa range from 100 to 150 lbN/acre
Soybeans range from 20-40 lb/acre
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Nitrogen Fixation is Difficult and Specialized

• N2 6H2 2NH3
• Fixing N2 is energetically expensive
• N N Triple bond
• Must use energy to break these bonds

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Artificial Nitrogen Fixation

• Haber - Bosch Process - Artificial Fixation of
  Nitrogen Gas
• 200 atm
• 400-500 oC
• no oxygen

yield of 10-20
Produces 500 million tons of artificial N
fertilizer per year. 1 of the world's energy
supply is used for it Sustains roughly 40 of
the worlds population
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Nitrogen and Food
Food production has grown with population
Crop Varieties Fertilizers
70 of water used
Irrigated land expected to expand by 23 in 25
years
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Nitrogen Fertilization
NH4
NO3-
Negative Exchange sites
NO3-
Loss of Productivity Leaching to groundwater,
surface water
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Some Areas of Florida are Susceptible
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Approximately 250 million years ago
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Approximately 150 - 200 million years ago
Late Jurassic
Flooded, stable platform Subject to marine
sedimentation
FL platform/plateau
For the next several million years the platform
was dominated by carbonate sedimentation
Sedimentation settling of particles from a fluid
due to gravity
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Carbonate Deposition/Sedimentation
Marine Calcium and Magnesium Carbonate
CaCO3 MgCO3
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Between about 150 Mya and 25 Mya
Florida platform was a flooded, submarine plateau
dominated by carbonate deposition
CaCO3
FL platform
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The Eocene and Oligocene Limestone
The Eocene and Oligocene limestone forms
the principal fresh water-bearing unit of the
Floridan Aquifer, one of the most productive
aquifer systems in the world
Eocene 55 34 million years ago Oligocene 34
24 million years ago
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Marine Carbonates
carbonates
Prior to 24 Mya
Between 150 and 25 Mya, Florida was dominated by
carbonate deposition
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Continental Influences
highlands
Sediments
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Isolation of the Florida Peninsula
Sediments
Georgia Channel
Suwannee Current
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Events of the Late Oligocene Epoch, approximately
25 Mya
Raising of the Florida Platform
Lowering of Sea Levels, Interruption of Suwannee
Current
Suwannee Current
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Exposure of Limestone
The Oligocene marked the beginning of a world
wide cooling trend and lower sea Levels.
Erosion cavities Due to acidity
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Miocene Epoch began approximately 24 Mya
sediments
Rejuvenation of Appalachians, weathering,
increased sediment load
Sediments were sands, silts, clays
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Filling in the Georgia Channel
Sediments
Early Miocene ( 24 Mya)
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Sediments
Rising sea levels allow sediments to
become suspended in water and drift over the
platform
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Siliciclastics Covered the Peninsula
Sands And Clays
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Summary

• Deposition of Eocene/Oligocene Limestone (55 24
  Mya)
• Raising of the Florida platform
• Lowering of sea levels, interruption of the
  Suwannee Current
• Infilling of the Georgia Channel with sediments
  derived from
• Appalachian/continental erosion
• Sea level rise, lack of Suwannee current.
• Suspended siliciclastic sediments settle over the
  peninsula
• These sediments blanket the underlying limestone
  forming
• the upper confining layer for the Floridan
  Aquifer.

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Permeability the ease with which water moves
through material
Surface Siliciclastics (sandy) (highly permeable)
Unconfined aquifer is extensive throughout the
state of Florida
Low Permeability Confining Unit (poor water
movement)
Clays and Sands (low permeability)
The Floridan aquifer is a confined aquifer. The
water-bearing unit is permeable limestone.
Low permeability rock (confining)
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The Water-bearing Unit is Extremely Productive
Calcium Carbonate CaCO3
Magnesium Carbonate MgCO3
limestone
How does this material hold and deliver water?
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Carbonate Dissolution
Acid (H) dissolves calcium carbonate
Carbonates are made porous by acid dissolution
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Rainfall is naturally acidic
Carbon dioxide dissolved in water produces
carbonic acid
CO2 H2O H2CO3 (carbonic acid)
H2CO3 gt H HCO3-
Acid
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Acidity from rainfall reacts with CaCO3 and
dissolves the carbonate rock.
CO2 H2O H2CO3
H2CO3 gt H HCO3-
CaCO3 H HCO3- Ca2
(acid)
(solid)
(solution)
(solution)
Dissolution Cavities
Dissolution Cave
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Caves and Solution Cavities
Acid dissolves calcium carbonate
CaCO3 H HCO3- Ca2
Channels and Caves
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Karst Topography
Characterized by sinkholes, springs, depressions,
lakes
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Sinkhole Lakes
Florida is Dominated by Karst Topography
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Sinkhole formation depends on the material
overlying the carbonate water-bearing unit
Very thick clays gt 200ft.
Thin, sandy covering
Cohesive clays up to 200ft
Thick sands up to 200 ft thick and some clays
Miocene clays have been eroded and shaped
throughout their history resulting in extreme
variability in thickness across the state.
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The Importance of Sinkholes and Sinkhole Lakes
Hydrologic connections between the surface and
the underlying limestone are maintained.
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Florida Nitrates (NO3-)
Nitrates do not interact significantly with
soil material and can move rapidly to
groundwater.
What areas are particularly vulnerable?
The unconfined, surficial aquifer
Areas where natural groundwater recharge occurs
Areas where the aquifer confining unit is thin
are also particularly vulnerable.
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Lower Suwannee River Watershed

• residential and commercial septic systems in
  rural areas
• about 300 row crop and vegetable farms
• 44 dairies with more than 25,000 animals
• 150 poultry operations with more than 38 million
  birds

Nitrates
NO3 Drinking water standard 10 ppm
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Groundwater Nitrate Discharge to Rivers
Possible sources of nitrate in the ground water
in the vicinity of the river include fertilizer,
animal wastes from dairy and poultry
operations, and septic-tank effluent.
Flow
Nitrate concentrations were higher in the
measured springs than in the river.
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Next Phosphorus