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Last updated: April 27, 2019
The physical and chemical breakdown of dead organic matter:

  • Releases nutrients for plant uptake
  • Influences ecosystem carbon storage and therefore climate
  • Returns the bulk of carbon fixed by photosynthesis to atmosphere
  • Is the 1st step in SOM formation which affects soil properties

Decomposition consists of 3 Processes:

  1. Leaching by water (PHASE 1)
  2. Fragmentation by soil animals (PHASE 2)
  3. Chemical alteration by microbes  (PHASE 3)

Decomposition Leaching by water (Phase 1)

  • Transfers soluble materials
  • Moves water-soluble compounds (sugars, amino acids) away from decomposing material
  • Begins while leaves are still on plant
  • Most important early in decomp

Decomposition Fragmentation by soil animals (Phase 2)

  • Increases surface area for microbial attack
    • Fresh litter is protected from microbial attack
      • Bark, epidermis, or skin on exterior
      • plant cells protected by lignin in cell walls
  • Time period where there is an increase in population of microbes

Decomposition Chemical Alteration by Microbes (Phase 3)

  • Changes chemical composition of detritus
  • Breaks down OM into CO and nutrients2
  • Forms complex recalcitrant compounds
    • Recalcitrant: “stubborn”

Comparison of Cell organics Glucose
Easily broken apart into Carbon Dioxide
Comparison of cell organics Cellulose

  • Slightly more complex
  • Specialized enzymes are necessary for breakdown

Comparison of Cell Organics Lignin

  • Very complicated structure
  • Common component in bark and some leaves
  • Very resistant to decomp

Decomposers Who are they and Why do they do it?

  • Decomposer organisms are subject to natural selection
  • Decomp is result of their feeding activity and population dynamics
  • C-cycling and nutrient mineralization are byproducts

Major Players in Decomp Fungi In Aerobic Environments

  • Account for most decomp in aerobic environments
  • 60-90% of microbial biomass in forests
  • ~50% of microbial biomass in grasslands

Major Players in Decomp Fungi Broad enzymatic capability

  • Cell walls: lignin, cellulose, hemicellulose
  • Main lignin degraders
  • cell contents: proteins, sugars, lipids

Major Players in Decomp Fungi Anatomy & Physiology

  • Composed of long networks of hyphae
  • Transport metabolites through hyphae
    • Surface litter: import N from soil
    • Wood degraders: import N from soil
    • Mycorrhizae: plants trade carbohydrates for nutrients/minerals from fungi

Major Players in Decomp  Bacteria Specialists

  • Spatial specialists
    • Rhizosphere, macropores, interior of soil aggregates
    • Form biofilms on partical surfaces
  • Chemical specialists
    • Different bacteria produce different enzymes (consortia)

Major Players in Decomp Bacteria Dependence on substrates

  • Dependent on substrates that diffuse to bacterium (not like fungi)
  • Become inactive when substrate is exhausted
    • 50-80% of soil bacteria inactive
  • Activated by presence of substrate
    • E.g., when root grows past

Major Players in Decomp Bacteria  

  • Grow rapidly: live fast, die young
  • Specialize on labile substrates
  • Some function anaerobically


Major Players in Decomp Microfauna Protozoans

  • Protozoans: Ciliates, amoebae
    • Aquatic, mobile
    • Bacterial predators (phagocytosis)
    • Rhizospheres specialists

Major Players in Decomp Microfauna Nematodes & Mites

  • Nematodes: many trophic roles
    • Extremely abundant
    • Often eat as much as above-ground grazers
  • Mites: many trophic roles
    • In Acari group, similar to spiders
    • Feed on bacteria and fungi

Major Players in Decomp Mesofauna 

  • Animals with greatest effect on decomp
  • Fragment litter
  • Ingest litter particles and digest the microbial jam

Major Players in Decomp Mesofauna Collembolans

  • Aka Springtails
  • Important mesofauna in Northern soils
  • Mainly feed on fungi

Major Players in Decomp Macrofauna 

  • Consists of: earthworms, termites, etc
  • Fragment litter or ingest soil

Major Players in Decomp Macrofauna Ecosystem Engineers

  • Mix soil, carry OM to depth
  • Reduce compaction
  • Create channels for water and roots

Major Players in Decomp Macrofauna Soil Animals

  • Collectively account for only 5-10% of soil respiration
  • Major impacts on decomp are indirect:
    • Alter soil environment
    • Graze on bacteria and fungi
    • Excrete N and P


  • High inputs of labile C “prime decomposition
  • Microbes break down SOM for N

Rhizosphere is theMAJOR ZONE OF DECOMPOSTION Microbial Processes

  • Bacterial starvation
  • Predation by protozoans
  • Rapid bacterial growth

Rhizosphere is theMAJOR ZONE OF DECOMPOSTION Root Processes

  • Nitrogen uptake
  • Root exudation
  • Sloughing of root cap


  • Declines almost exponentially with time
    • Rates differ among different substrates (branch, leaf, needle)
  • Lt = L0e-kt

LITTER MASS  Meaning of variables

  • L0: mass at time zero
  • Lt: mass at time t
  • k: decomposition constant
    • Litterfall/litterpool (at a steady state)
  • 1/k: mean residence time
  • kt: negative because litter mass is expected to decline over time

LITTER MASS  Litterfall vs.


  • Litterpool: steady amount of litter throughout the year
  • Litterfall: altered throughout the year
  • Use litter bags to measure
    • bages filled with typical amounts of litter

LITTER MASS  K is not constant over time:

  • Due to composition changes
    • Phase 1: leaching dominates
    • Phase 2: high value of K, labile substrates broken down by fragmentation plus chemical alteration
    • Phase 3: low value of K, recalcitrant substrates predominate
    • Time scale depeds on environment (tropics vs. arctic)

LITTER MASS  Olsen (1963)

  • Decomposition rates:
    • Highest: warm and moist
    • Lowest: cool and/or dry    OR    cool and/or wet

CONTROLS OVER DECOMPOSITION  1. PHYSICAL ENVIRONMENT Direct Temperature effect on microbial activity

  • Temp optimum much higher than ambient temp
  • Maintenance respiration: increasing proportion of total at high temp (high temp not necessarily optimal for microbes)
  • Growth respiration dominates at optimal temp, but maintenance respiration increases with temp
  • Temp Fluctuations: freeze-thaw lyses microbes, increases substrate supply


  • Effects of evaporation and soil moisture
  • Effects on quantity and quality of litter inputs


  • Response to decomp to moisture is similar to that of photosynthesis: declines at extremely low/high moisture
  • Less sensitive to low moistureNo litter accumulation in deserts
  • More sensitive to high moisture:  SOM accumulation in waterlogged soils


  • Bacteria predominate at high pH
  • Fungi predominate at low pH
  • Lower rates at lower pH


  • Protection of SOM by the large surface area of clay layers
  • Aggregate structure (anaerobic microsites)
  • Some chemical groups unavailable to enzymes when OM binds to clay particles



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  • Reduces SOM protection by clays
  • Breaks up soil aggregates
  • Increases aeration

CONTROLS OVER DECOMPOSITION  1. Substrate Quantity & Quality 
THE major controls over decomposition NPP: Net Primary Productivity
CONTROLS OVER DECOMPOSITION 2. Substrate Quantity & Quality Substrate Quality  

  • Susceptibility to decomp
  • THE predominant control over decomp
    • Climate exerts large effect on substrate quality through effects of vegetation

CONTROLS OVER DECOMPOSITION 2. Substrate Quantity & Quality  Substrate Quality   Depends on:

  1. Size of a molecule
  2. Types of chemical bonds
  3. Regularity of structure
  4. Toxicity
  5. Nutrient concentrations

CONTROLS OVER DECOMPOSITION 2. Substrate Quantity & Quality  Substrate Quality   Depends on: Size of a Molecule

  • Large molecules (cellulose, proteins) must be broken down outside cells
  • Limits metabolic control that microbes can exert over breakdown processes
  • Requires production of exoenzymes
  • Comparison of cell organics
    • Glucose → Cellulose → Lignin


Substrate Quantity & Quality  Substrate Quality   Depends on: Types of Chemical Bonds

  • Some bonds are easier to break than others:
    • Peptide bonds compared to aromatic rings
    • Most litter N (80%) in proteins
    • Most N is in old SOM

CONTROLS OVER DECOMPOSITION 2. Substrate Quantity & Quality  Substrate Quality   Depends on: Regularity of Structure

  • Lignin and humus have irregular structure

CONTROLS OVER DECOMPOSITION 2. Substrate Quantity & Quality  Substrate Quality   Depends on: Toxicity

  • Phenolics evolved to protect plants from herbivores and pathogens
  • May affect decomposers
  • Importance of this effect is uncertain

CONTROLS OVER DECOMPOSITION 2. Substrate Quantity & Quality  Substrate Quality   Depends on: Nutrient Concentrations

  • Nutrients are essential to support microbial growth


  1. Physical Environment
  2. Substrate Quantity and Quality
  3. Properties of Microbial Community


  • Mineralization: decomp of SOM by soil microbes releasing mineral N in the process
  • Immobilization: Conversion of mineral N to organic N by microbes
    • Organisms that decom OM as an energy source require N


  • CO2 released as byproduct
  • C:N ratio is high in beginning
    • Becomes smaller, leaving most mineral N behind (decreases exponentially)
  • Microbial biomass reflects C:N ratio


  • Index of ratio of cytoplasm to cell walls
  • Measure of N concentration
  • Directly affects decomp mainly in the presence of labile C


  • Integrated measure of N concentration and substrate size/complexity
  • As the ratio in hardwood leaf litter increases, decomp rates decrease

 Plant species differ predictably in litter quality

  • High-resource-adapted leaves decomp quickly due to higher concentrations of labile C and N
  • High-resource-adapted plants grow quickly when resources are available and die quickly with resource exhaustion
    • Not invested in making compounds, making them resistant to decomp

 Substrate Quality of SOM

  • Much of SOM is old & recalcitrant
  • Consists of “leftovers” and microbial products
  • Density and particle size fractionations can distinguish pools with different turnover rates
  • Ligh, particulate SOM (>53mm) decomposes faster than dense, silt+clay SOM

  Long-term Storage of SOM: Humification

  • Formation of SOM that doesn’t decompose easily
  • Critical determinant of soil properties


  • Quantity ; Quality of litter input
  • Environmental conditions that favor biological activity
  • Microbial activity is more important than microbial mass

;Soil respiration correlates closely with rates of Photosynthesis

  • Some is decomposition: depends on litter quantity ; quality
  • Some is root respiration: correlates with photosynthesis

;;Decomposition in Aquatic Environments

  • Depends on stability of environment (intertidal)
  • Flowing water
    • Shredders: aquatic anthropods, fragment organic particles, eat bacteria/fungi on litter surface
    • Collectors: clams, mussels, filter water
    • Grazers/Scrapers: feed on algae, bacteria, fungi, and OM collected on rocks and debris

;AQUATIC ORGANIC MATTER;Particulate Organic Matter (POM)

  • Poorly available, Large organic particles
  • Humic compounds in substrate
    • Low O at bottom of still water: very low decomp
  • Ratio of anaerobic respiration to aerobic respiration is high

;AQUATIC ORGANIC MATTER;Dissolved Organic Matter (DOM)

  • Readily Available
  • Small suspended/dissolved organic compounds
  • Excretia of phytoplankton, macroalgae, zooplankton
  • Bodies dissolve rapidly upon death
  • Substrate for bacterial growth
    • Reconcentration of OM

;;Benthic Zone vs. Photic Zone

  • Photic zone: top of water system
    • Where decomp occurs
  • Benthic zone: bottom of water system
    • Very low O
    • Little to no decomp


  • Major avenue of carbon loss from ecosystems
  • Determined primarily by factors regulating photosynthesis
  • Sensitive to global change
  • Has potentially large feedbacks to climate

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