Organisms

Soil Organisms

The soil is alive!

There may be > 4 trillion organisms per kilogram of soil and more than 10,000 different species in one gram of soil.

There is considerable variability in the size of various microbial populations due to differences in soil, climate, vegetation and management. Microbial populations are dynamic and often vary by factors of ten. Below are typical populations based on per gram of soil, grams per square meter and the weight of found in an acre furrow slice (AFS) of soil.

	Number (g soil)	Biomass^† (g/m²)	Biomass^‡ (lbs/AFS)
Bacteria/Archaea	10⁸ – 10¹⁰	40 – 500	250 – 2,500
Actinomycetes	10⁶ – 10⁸	40 – 500	250 – 2,500
Fungi	10⁵ – 10⁶; 10 – 10³ m^‡	100 – 1500	450 – 4,500
Nematodes	10¹ – 10²	1 – 25	1 – 100
Protozoa	10³ – 10⁵	1 – 50	5 – 200
Earthworms	<1	5 – 200	10 – 1000
Algae	10² – 10⁵	5 – 500	10 – 1500
Viruses	10¹⁰ – 10¹¹

^†Biomass is reported on a live weight basis; dry weight would be approximately 25% of the value.
^‡It is difficult to discern individual fungi; hyphal length is a better estimate of abundance.

Soil organisms consist of both plants (flora) and animals (fauna). Some may be seen by eye (macroorganisms) while others can be seen only with the aid of a microscope (microorganisms).

The general classification of soil organisms. Many classification schemes exist for classifying soil organisms, but we will just be concerned with the broad categories.

Soil organisms may be classified on the basis of their source of energy and carbon:

Autotroph: An organism that need not take in organic food to get energy. For example, a photoautotroph uses light, and a chemoautotroph obtains energy from oxidation of inorganic substances such as nitrogen, sulfur, and iron. See heterotroph as a contrast.

Heterotroph: (decomposers) - Organisms which derive energy for their growth only from the decomposition of organic compounds. These organisms are more abundant than autotrophs and are responsible for most of the decay process (e.g., most bacteria, fungi, actinomycetes, and HUMANS).

Some examples of Soil Macroanimals

Earthworms - >7000 species; some are up to 10 feet long!

ingest organic matter and microorganisms for their nutrition
ingest a weight of soil 2 to 30 times their own weight each day
thrive in the upper 15 to 35 cm of moist, well aerated soils with high calcium and moderate pH values (5.5 to 8.5)

Termites - ≓ 2000 species;

major roles are breakdown of organic matter and mixing of soil
most prominent in grasslands and forests of the tropical and subtropical areas
microorganisms in their gut assist in the decomposition process
bacteria in their guts are responsible for a large fraction of the global production of methane, an important greenhouse gas.

Ants - ≓ 9000 species

especially active in humid tropical areas
feed on organic matter, living plant tissue or other soil organisms

Important roles of macroanimals

Physically breakdown organic materials exposing more surface area
Increase aeration and improve drainage
Mix and granulate the soil
Increase the size and stability of soil aggregates

Some examples of Soil Microanimals

Nematodes - 4-100 μm in cross-section and a few millimeters in length

most are predatory on other nematodes, fungi, bacteria, etc., but some infect (eat) the roots of plants and may cause crop damage

Protozoa - ≓ 350 species; 6 - 10 μm in diameter

primarily eat soil bacteria by capturing and engulfing them; many cause serious animal and human diseases

Soil Plants

Roots of higher plants are a major source of organic matter in soils, especially in grassland soils.
Rhizosphere is the zone of soil significantly influenced by living roots (≓2 mm zone around root); this zone has a lower pH, higher organic matter (root exudates) and increased microbial activity.

Algae: An aquatic, eucaryotic, plantlike, photosynthetic organism, mostly microscopic, often single celled.

Many algae contain chlorophyll and are thus capable of photosynthesis (found near the soil surface)

Lichens: Symbiosis between fungi and algae or bluegreen bacteria, commonly forming a flat, spreading growth on surfaces of rocks, tree trunks, and soil.

Soil stabilization.

Fungi: Eukaryote microorganisms with a rigid cell wall. Some form long filaments of cells called hyphae that may grow together to form a visible body.

Tens of thousands of species; most are heterotrophs
dominant microorganism under acidic conditions
many cause disease in plants (damping off disease)
some produce valuable antibiotics (penicillin)

Mycorrhizae: A, usually, symbiotic association between fungi and the root of a higher plant.

Ectomycorrhiza: A symbiotic association between fungi and plant root. Hyphae form a sheath around the root but the hyphae form an entirely intercellular interface–no cell penetration–between epidermal and cortical root cells (Hartig net).

Endomycorrhiza: A Symbiotic association between fungi and plant root. Hyphae penetrate directly into root hairs and epidermal cells and oasionally into cortical cells.

Arbuscular enodmycorrhiza: The fungal hyphae also form a structure known as a Hartig Net into the outer cortical cells similar to ectomycorhiza. The sheath can also function as a place to store excess nutrients, at times when nutrient levels are running low the fungi can release the stored nutrients into the plant. The major difference between ectomycorrhizal fungi and arbutoid fungi is that the hyphae of the arbutoid fungi do in fact penetrate the outer cortical cells of the plant root forming arbuscules within the plant cell.

Symbiosis: Two dissimilar organisms living together in intimate association; the cohabitation is often mutually beneficial to each organism.; Fungi receive sugars and other organic exudates from root for use as food. In return the fungi provides the roots with enhanced availability of several essential nutrients (e.g., phosphorus, copper, and iron), increased amounts of water, and protection from some pathogens (from antibiotics) and toxic metals. The increased water and nutrient availability is thought to result from the increased surface area provided by the fine filamentous hyphae of the fungi (approx. 10 times the surface area of the root alone) and by production of organic acids, chelates and enzymes by the fungi.

Actinomycetes: Filamentous and profusely branched bacteria that form a thin, elongated, connect and branching pattern similar in appearance to fungal hyphae. Phylum Actionbacteria, order Actinomycetales.; Actinomycetes perform symbiotic N fixation in woody plant (e.g., alder and ceanothus) and they produce many wonder drugs (streptomycin).

Archaea: One of two domains of single celled organisms. These microorganisms are prokaryotes and have no cell nucleus. Archaea reproduce asexually by binary fission, fragmentation, or budding. Archaea use more energy sources than eukaryotes and include species that are adapted to extremes of salinity and heat and some subsist on methane. Some can fix carbon and some can use sunning as an energy source but none are known to do both.

Bacteria: One of two domains of single celled organisms. These microorganisms are prokaryotes and have no cell nucleus.

≓ 0.5 to 5 μm
most diverse group of soil organisms
single celled
1 gram of soil typically contains 20,000 different species
adapted to the most extreme environments on Earth
a soil may contain more than 2 trillion per kilogram
both autotrophic and heterotrophic
can double their population in 2-3 hours
Rhizobium species - nitrogen fixers on legumes
cyanobacteria (formerly known as blue-green algae) can fix large amounts of atmospheric nitrogen (e.g., rice fields)

Optimum conditions for growth of bacteria

These can also be used to categorize the organisms.

Oxygen requirement
1. Aerobic - must have oxygen
  1. In most cases, optimum oxygen ranges from atmospheric levels (21%) to about 10%.
  2. < about 10% O₂, many aerobic processes such as decomposition begin too slow.
  3. Protozoa and nematodes need water in which to move, but O₂ for respiration.
2. Anaerobic - no oxygen can be present
3. Facultative - can utilize both aerobic and anaerobic metabolism
Moisture relationship
1. Optimum moisture level is generally near field capacity (Ψ_m = -0.1 to -0.3 bars)
2. Can maintain low activities even at very low moisture contents (down to Ψ_m = -35 bars)
3. Moisture content affects oxygen supply
Temperature range
1. Bacteria activity is generally greatest at 20 to 40℃ (70-100℉)
2. Activity is very slow at temperatures less than 5 ℃
  1. In general microbial activity increases as temperature increases until temperature starts to interfere with microbial integrity (denature proteins, etc.).
  2. As soil temperature increases from 0 ℃ to about 15 ℃ there is a linear increase in decomposition rate.
  3. From 15 ℃ to about 40 ℃, the decomposition rate increases 2 to 3 times for each 10 ℃ increase in temperature. (Similar to Van't Hoff's Rule).
  4. Above about 40 ℃, decomposition rate may decline unless the soil microbial population is acclimated to high temperatures.
3. three broad groups of microorganisms which tend to dominate the overall microbial populations within three temperature ranges:
  1. < 15 ℃ (psychrophiles).
  2. 15 to 40 ℃ (mesophiles, the majority of soil organisms).
  3. > 40 ℃ (thermophiles).
  4. Within each group of microorganisms there is a minimum, maximum and optimum temperature for their growth and metabolism
  5. Most microbial activities are optimum between 25 and 35 ℃.
4. At temperatures below ℃ (50 ℉), very little nitrification occurs.
Organic matter requirements
1. Organic matter is used as an energy source for the majority of bacteria (heterotrophic)
2. SOM associated N and P nutrients
  1. There is a more rapid release of N for low C:N ratios.
  2. Net N mineralization for C:N values of < 25:1
  3. Net N immobilization for higher C:N ratios
  4. P Mineralization is rapid if the C:P ratio is < 200.
  5. P Mineralization is quite slow if the C:P ratio is > 300.
3. Organic matter is not required as an energy source for other bacteria (autotrophic)
Exchangeable calcium and pH
1. High calcium concentrations and pH values from 6-8 generally are best
2. Calcium and pH play a major role in determining the specific bacteria present
3. Certain bacteria function at very low pH (<3.0) and a few at high pH values (>10)

Important beneficial activities of soil organisms

Decomposition of organic residues with release of nutrient elements (mineralization)
- Organic Matter + O₂ ⟶ CO₂ + H₂O (The respiration process)
- Organic Matter ⟶ nutrients (Mineralization process)
Formation of soil humus through decomposition and synthesis reactions Organic Matter ⟶ humus (Humus formation process)
Improvement of soil physical properties (e.g., soil structure, drainage, aeration, bulk density)
Release of plant nutrients from insoluble inorganic soil minerals (production of chelates)
Fixation of nitrogen from atmosphere
- (e.g., Rhizobium on legumes, Frankia on alder) N-fixation N₂ + 3 H₂ ⟶ 2 NH₃
Improved nutrient and water availability through mycorrhizal relationships
Antagonistic action against plant pathogens (production of antibiotics)
Breakdown of toxic compounds (bioremediation - breakdown of PCB’s, pesticides, etc.)

Role in soil biochemical reactions:

Nitrification NH₄⁺ + 2 O₂ ⟶ NO₃¯ + H₂O + 2 H⁺
Oxidation/Reduction of inorganic elements:
Fe³⁺⟶ Fe²⁺
NO₃¯ ⟶ N₂ (gas) (denitrification)

Deleterious effects of soil organisms

Soil fauna eat agricultural and garden produce (e.g., slugs, snails, nematodes, aphids)
Plant diseases - wilts, damping-off, root rots, blight, and rusts by fungi (most important), bacteria, & actinomycetes
Competition for nutrients - nitrogen deficiencies can result from microbial theft of available nitrogen when organic materials with a high C/N ratio are applied
Mediation of oxidation/reduction reactions: Denitrification in the absence of oxygen: NO₃¯ ⟶ N₂ (gas) NO