Soil Biology

1. Types of organisms
2. Organisms in action
3. Organism abundance, biomass, and metabolic activity
4. Earthworms
5. Termites and ants
6. Soil microanimals
7. Roots of higher plants
8. Algae
9. Fungi
10. Actinomycetes
11. Soil bacteria
12. Conditions affecting growth of soil bacteria
13. Competition
14. Effects of agricultural practices
15. Beneficial effects of soil organisms
16. Injurious effects of soil organisms on plants

1. Types of organisms

A. Grouped according to animals (fauna) and plants (flora)

  • subgrouped by body size

  • macro: visible to the eye
  • meso: bordering on microscopic
  • micro: microscopic

B. Functionally classied by feeding habits

  • herbivores (H)
  • detritivores (D)
  • predators (P)
  • bacterivores (B)
  • fungivores (F)


C. Organisms can also be classified according to how they obtain energy and carbon to grow

Sunlight energy:
  • plants
  • algae (microplants)
  • some bacteria (cyanobacteria or "blue-green algae")

Mineral energy:
  • Includes all fauna and most microflora except some bacteria (autotrophs)


D. Some bacteria can grow in the absence of air (oxygen)

  • Anaerobes continue decomposition and other mineral cycling processes in flooded soil

2. Organisms in action

A. Activity catagories

  • Primary producers: Form basis of the soil food web, produce the organic materials that all other organisms (heterotrophs) feed on

  • Primary consumers: Organisms feeding directly on plants or plant products

  • Secondary, tertiary consumers: Feed on other organisms (heterotrophs) or their waste products

B. Primary consumers

Bacteria and fungi:
  • feed directly on dead and live plant material (parasites)

Collembola, other arthropods:
  • feed on plant litter, physical disruption breaks material into smaller pieces that are more readily decomposed by bacteria and fungi

  • feed on detritus and breakup plant material

  • Mechanical activity of meso-/macro-fauna on enhancing litter decomposition

C. Secondary, tertiary consumers

Bacteria and fungi:
  • feed on bacteria and fungi (that may be feeding on plant material)

Collembola, other arthropods:
  • feed on fungi, nemtodes

  • feed on detritus and breakup plant material

3. Organism abundance, biomass, and metabolic activity

  • Measures of soil community composition
  • abundance: numbers of individuals
  • biomass: weight of selected groups of organisms
  • metabolic activity: pace at which processes may be occuring
  • All of these measures vary in space and time. Measurements for any of these may vary depending on which patch of soil you look at and the time of year that it is examined

  • Generalizations: Higher organic matter (more food) = higher biomass, organism abundance, and activity

4. Earthworms

A. Biology

  • Annelid = "ringed", refering to series of rings that compose their bodies

  • Almost 2,000 species known, the familiar "night crawler" (Lumbricus terrestris) was introduced in North America with transplanted european trees, and has since come to dominate over the native species

B. Soil fertility and productivity

  • Earthworms eat through soil, the trail of digested material is referred to as casts

  • In one day, a single earthworm may consume 2 to 30 times it's own weight in soil, estimates of amounts of soil processed by worms range from 22 to 450 tons/acre

  • Earthworm activity creates a network of burrows, and large masses of soil enriched with nutrients and other properties favorable to soil fertility

C. Physical effects:

  • Burrows increase aeration and drainage, may improve conditions in compacted soils

  • Casts stabilize soil on surface, less erodable than non-processed soil.

D. Chemical leaching:

  • Improved drainage may be harmful as it may allow rapid movement of chemicals to the subsurface and groundwater contamination

  • Worms may decrease residue cover of surface and thus increase surface run-off

E. Factors affecting earthworms:

  • Earthworms prefer soils that are cool (50 oF) moist, well-aerated and have a ready supply of organic matter

  • burrow deep into soil to avoid heat, cold, or dessication

  • Applications of chemicals (fertilizers, pesticides) and intensive tillage may decrease numbers

  • Most abundant in medium texture soil

5. Termites and ants

A. Biology

  • Soil burrows provide a moist, humid environment that ants and termites need to survive

B. Effects on soil physical-chemical properties
  • Contribute to decomposition of organic matter on the soil surface

  • Complex subsurface tunnels, activity contributes to the mixing of surface and deeper soil; soil mixing from ants estimated at 6 tons per acre per year

  • In subtropical/tropical areas, soil mixing effects of termites may be more important than those of earthworms
C. Soil productivity
  • Effects of termites are not as significant as digestive processes are more complete. Also, termite activity is more localized while that of the worms distributed across soil surface

  • Mound material may alter surface soil characteristics as these are built from subsurface material

  • Termite hindguts colonized by anaerobic bacteria that form methane; a significant global source of methane (greeenhouse gas)

6. Soil microanimals

Soils are partially aquatic, having thin water films in which microscopic organisms live

A. Nematodes

  • (also called eelworms, threadworms) can be seen only with the aid of a microscope

  • Nematodes are diverse in feeding habit, being bacterio-, fungi-, or detritovores

  • Some nematodes are plant parasites and can cause damage to a wide variety of crops

  • Nematodes feeding preferences may be deduced from their mouth parts

  • Nematodes have been controlled by fumigating soil with methyl bromide

  • Concerns over damage to ozone layer from methyl bromide have resulted in legislation calling for a phase-out and ban by the year 2000. This is a controversial ruling because of the potential economic impact and lack of alternative pest-control agents

B. Protozoa

  • Graze on microbial populations particularly bacteria, which they capture by engulfment

  • A variety inhabit soils, classified according to their method of movement

  • Amoeba (move by pseudopods),
  • Ciliates (vibration/waving of hair-like structures),
  • Flagellates (waving of flagella)

  • A number of human diseases are caused by protozoans, but those inhabiting soil are harmless

7. Roots of higher plants

  • Plants are the foundation of soil food webs
  • above ground litter drop
  • below ground release of organic compounds from roots Release organic materials that are utilized by bacteria and fungi, which are grazed by protozoa and nematodes

    Roots create channels to the surface that allow air/water penetration

A. Root morphology

  • May be viewed as either macro- or meso-organisms
  • macro: "feeder roots" active in nutrient uptake (100 to 400 um diam.)
  • meso: "root hairs" (10 to 50 um diam.); serve as anchor points during growth
  • Root tip: growing point of the root; covered by the root "cap", a protective cell layer

B. Amounts of organic matter added

  • Roots input substantial amounts of organic material to soil during and after growth
  • The quantity of roots remaining after crop harvest may be 15 to 40% of the plant biomass
  • Assuming an average of 25%, amounts of root material deposited are (kg/ha):
  • oats: 2,500
  • corn: 4,500
  • sugarcane: 8,500

C. Rhizosphere
  • Roots alter physical-chemical characteristics of adjacent soil from that of the "bulk soil"

  • Size varies, often estimated at 1-2 mm

  • "Rhizodeposition": release of organic materials from roots

  • Types of rhizodeposition materials
  • Low molecular weight compounds (sugars, amino acids, etc.) general stimulation of microbial growth; stimulatory/inhibitory effects on particular organism ("allelopathy")
  • High molecular weight "mucilages"; gel-like materials
  • Sloughed cells; old cells from root cap

  • Collectively, these materials may be 1 to 30% of the total dry matter of young plants
  • Rhizodeposition decreases as plants mature

8. Algae

  • Photosynthetic organisms, contribute to soil primary production

  • Abundance and activity is strongly influenced by the soil moisture level

  • May have beneficial effects on soil physical properties by producing gums that cement soil particles together and improves soil aggregation

9. Fungi

  • plant-like (eucaryotic) cell structure
  • hetertrophs (non-photosynthetic)
  • A diverse collection of oragnisms, major groups are the yeasts, molds and mushrooms

A. Yeasts

  • Single-celled
  • Can survive under conditions of very low or no oxygen.

B. Molds, mushrooms

  • Filamentous; form strands of connected cells called "hyphae"
  • Masses of hyphae form "mycelia", which may be visible to the unaided eye.
  • Mushrooms form large above-ground fruiting structures

  • Molds form microscopic fruit structures

C. Activities of fungi

  • Decomposition of residues, particularly woody materials and animal wastes
  • Hypahe join soil particles into aggregates

  • Consumption of nematodes: some fungi trap nematodes with constricting rings or adhesive nodes and then digest their prey

D. Mycorrhizae

  • An important beneficial plant-microbe interaction is the symbiotic association of mycorrhizal fungi with plant roots

  • Symbiotic = both organisms benefit. Fungus gets direct acces to organic material produced by the plants. Plants have improved nutrient and water uptake

  • These associations are very common, and are important to the growth/survival of plants in some soils

  • Two types of mycorrhizae are the ecto- and endo-mycorrhizae, distinguished based on physical association with plant root
i. Ectomycorrhizae form mantels around plant roots and associate mainly with tree species (pine, birch, oak, spruce). These may also live free in the soil

ii. Endomycorrhizae form structures that penetrate into the plant root cells; arbuscles (nutrient transfer) and vesicles (nutrient storage)
  • Endomycorrhizae thus also known as the vesicular-arbuscular mycorrhizae (VAM)
  • VAM are associated with a wide variety of plants including agronomic crops (corn, wheat, beans), vegetables, fruits (apples, grapes, citrus), and trees (maple, redwood)
  • VAM are obligate symbionts

10. Actinomycetes

  • A subset of bacteria, distinguished by their formation of cell-chains that form filaments similar to those of fungi

  • Smaller than fungi and have a cell structure like that of bacteria (procaryotic)

  • Wide-spread soil inhabitants, their abundance relative to the bacteria as a whole decreases with decreasing pH and decreasing oxygen levels

11. Soil bacteria

  • Most abunadant group of organisms in soil

  • Grow as individual cells

  • Can be observed directed in soil with the aide of flourescent stains

  • Some bacteria use minerals as food (energy) sources making them key components in the cycling of almost all elements

  • N cycle example bacteria using ammonia as an energy source catalyze nitrification (conversion of ammonia to nitrate)

12. Conditions affecting growth of soil bacteria

  • Oxygen
  • Moisture
  • Temperature
  • Organic matter
  • Exchangeable nutrients and pH

13. Competition

  • Soil environment is resource limited. Resources = energy sources (organic material) and/or other nutrients

  • Competition may be that organisms are able to exploit a resource faster than its neighbors or perhaps simply get by with less

  • They may also attempt a pre-emptive strike and produce compounds that inhibit the activity of potential competitors by producing antibiotics

14. Effects of agricultural practices
  • Soil organisms are affected to natural enironmental fluctuations and those resulting from human activities

  • Pesticides like methyl bromide may have adverse effects on organisms in addition to those targeted

15. Beneficial effects of soil organisms

  • Organic matter decomposition
  • Microbes ultimate recyclers of the organic material produced by plants
  • By-products have favorable effects on soil struture and plant nutrition
  • Degradation of toxic compounds
Activities are an out-growth of natural degradation processes, and form the basis for bioremediation
  • Transformations of minerals
Key to element cycling. May also be involved in elimination of toxic metals
  • Nitrogen fixation
Nitrogen is a essential element used by all orgnaims in the building of a wide variety of life-supporting compounds
  • Inhibition of plant pathogens
Nitrogen is a essential element used by all orgnaims in the building of a wide variety of life-supporting compounds.

16. Injurious effects of soil organisms on plants

  • Persistence of plant pathogenic organisms (insects, nemtaodes, fungi, bacteria) in soil
  • may be controlled by pesticides or soil management (crop rotation) to reduce the size of the soil population

  • Competition for nutrients
  • microbes more effectively absorb nutrients and "immobilize" these in their biomass