Chapter 7: Organisms


A biological universe exists in a gram of soil.

Biological Classification


A soil aggregate or ped is a naturally formed assemblage of sand, silt, clay, organic matter, root hairs, microorganisms and their secretions, and resulting pores.

A soil aggregate or ped is a naturally formed assemblage of:

  • sand
  • silt
  • clay
  • organic matter
  • root hairs
  • microorganisms and their secretions
  • pores



Soil Biota

Consists of:

  • bacteria
  • fungi
  • algae
  • soil animals
  • plants

Millions of species of soil organisms exist but only a fraction of them have been identified.


Soil biota can be grouped by size classes:

  • macrofauna (cm)
  • mesofauna (mm
  • microfauna (μm)



Soil Communities





Requirements and Adaptations of Microbes


Nutritional Requirements of Organisms in General

Kinds of Organisms in the Soil

Kind Food Energy source
Large Eucaryotes
  • Animals
  • Plants

Solid organic
CO2 + ions

Oxidation of organics

Small Eucaryotes
  • Protozoas
  • Algae
  • Fungi

Solid & dissolved organics
CO2 + ions
Dissolved organics


Oxidation of organics
Oxidation of organics
  • Phototrophic
  • Chemotrophic
  • Heterotrophic

CO2 + ions
CO2 + ions
Dissolved organics



Oxidation of inorganics
Oxidation of organics




Heterotrophic organisms get energy from reactions involving organic substrates such as sugars.


The energy is released by:

  • respiration
  • fermentation




Plant root systems function heterotrophically but the plant as a whole is autotrophic.

Oxidation Processes That Supply Energy to Microbes

Reductant Oxidant Products Organism/conditions
Sugars and other organic compounds


CO2 Most organisms, aerobic
Sugars and other organic compounds   CO2, N2, N2O Denitrifiers*, low O2
Sugars and other organic compounds   CO2, S S reducers**, low O2
Sugars and other organic compounds Oxygen CO2, organic acids Anerobic fermenters/low O2
NH4+, NO2- Oxygen N2O-, NO3- Nitrifiers/aerobic
S Oxygen SO42- S oxidizers/aerobic
Fe2+ Oxygen Fe3+ Iron bacteria/aerobic

* Denitrifier: microbial process of nitrate reduction

** (S)ulfur reducers: get their energy by reducing elemental sulfur to hydrogen sulfide




Heterotrophs and autotrophs depend on each other.

The cycling of nutrient elements depend on these organisms.




Large Organisms

Plants & Their Roots





  • Meristem
  • Stele
  • Xylem
  • Phloem
  • Root hairs
  • Epidural cells


The rhizosphere contains a dynamic and continuously changing biological community that may include:

and larger organisms such as:


Soil Biology Movies



Transparent Soil

transparent soil, nafion, university of abertay dundee, uk, roots, rhizosphere, James Hutton Institute



root, tip, microscope, rhizosphere, nafion, transparent soil