CHAPTER VI – Soil Biology and Organic Matter

Thing to remember: “Microbes Rule the World”

Macrofauna

1. Vertebrates (e.g. rodents)

2. Annelids
e.g. Earthworms

1. process up to 15 tons of casts/Acre/year

2. borings which may improve aeration and drainage
3. prefer moist, aerated, finer textured soils with pH around 6.5
3. Arthropods (insects, arachnids, crustaceans)
1. ants, termites, beetles, grubs, centipedes
2. contribute to early breakdown of organic matter (reduces the size of
larger organic materials)
4. Mollusks (snails,slugs)

Soil Microorganisms (Soil Microbes)

- Soil organisms that requires a microscope to observe and study

1. Microfauna
1. Nematodes (threadworms, eelworms)
 Eukaryotic and multicellular
 Have a body size of 200 to 1000 µm
 Typically slender, cylindrical and unsegmented
2. Protozoa (Amoeba)
 Less than 200 µm long
 Eukaryotic and unicellular
2. Microflora
1. Bacteria
 Simple, single-celled microbes, prokaryotic and most are heterotrophic
although there are many that derive energy autotrophically from
chemical reactions.
 most numerous microbes in the soil – 10 8 to 109 per gram of soil
 may pack up to 1,000 enzymes in their bodies (they are considered
micro bioreactors)
 “structurally simple but functionally complex”
 populations are dependent on food source and environment.
 Optimum moisture level for most plants are usually best for bacteria
2. Actinomycetes
 A special group of bacteria
 They look like fungi (filamentous) and has spores (conidia), but they are
like bacteria because they are prokaryotic and their walls are like that of
bacteria.
  2nd most abundant organism in the soil (over 1 million / gm)
 decompose resistant organic compounds(cellulose, lignin and chitin)
 like pH 6-7.5
 some fix Nitrogen (Frankia)
 give soil its rich earthy smell
 some produce antibiotics such as Streptomycin and Chloramphenicol
(from Streptomyces)
3. Fungi
 no chlorophyll -- heterotrophic organisms(energy from organic
compounds)
 fungi are fewer in number than bacteria but make up the largest
biomass of any microbe in soils. A mass of hyphae is called mycelium.
 Exists in a wide range of soil pH --- Molds (widest pH range)
 dominate at low pH due to reduced competition
 decompose cellulose, lignins and complex organic compounds
 Usually multicellular but may include unicellular organisms (yeast)

Mycorrhizal fungi- “Fungus-Roots” symbiotic association. The fungus

colonize plant roots in a symbiotic relationship utilizing
carbon from the plant while benefitting the plants by
increasing uptake of phosphorus and possibly other
nutrients and water.

Lichen- “Fungus-Algae” symbiotic association. The fungus provides

growth factors (water nutrients) to the algae while the
algae in return provide photosynthates to the fungi.
4. Algae
1. contains chlorophyll and are photosynthetic. They are autotrophic
organisms
2. primary producers
3. live near the soil surface (because they need light)
4. found in moist to wet soils at or near a neutral pH.
5. May live in leaves of aquatic fern, azolla

Microbial Groups with representative size and number (top 10 cm of soil)

Microbial Group Example Size (µm) Population density
(organisms per g soil)
Bacteria Pseudomonas 0.5 x 1.5 108-109
Actinomycetes Streptomyces 0.5 -2.0 107 -108
Fungi Mucor 8.0 105-106
Algae Chlorella 5 x 13 103 -106
Protozoa Euglena 15 x 50 103-105
Nematodes Pratylenchus 1,000 101-102
From: Sylvia et al., Principles and Applications of Soil Microbiology
 Distribution of microorganisms along a soil profile
Thousand of organisms per gram soil
Depth (cm) Aerobic Anaerobic Actinomycetes Fungi Algae
Bacteria Bacteria
3-8 7,800 1,950 2,080 119 25
20-25 1,800 379 245 50 5
35-40 472 98 49 14 <1
65-75 10 1 5 6 <1
135-145 1 <1 ND 3 ND
From: Mark Coyne, Soil Microbiology

Environmental Factors Affecting Microorganism Populations

1. Moisture Content: Moist soils around –Field Capacity is best for

microorganisms. Soil moisture conditions that are too dry or too wet inhibit
microbial activity.
2. Adequate Temperature Range: Activity of microorganisms is limited below 5
degrees C
 Psychrophiles: -5 to 25 oC
 Mesophiles : 15- 40 oC
 Thermophiles: 40-70 oC
 Hyperthermophiles: at least above 60oC, usually at 80 – 100 oC
3. Adequate Carbon: Organic matter is a food source. Different organisms use
different types of organic matter
4. Adequate Soil pH: Different microorganisms work in specific pH ranges.
 Bacteria prefers near neutral pH and is adversely affected by acidic
conditions
 Fungi are more resistant to acidic conditions.
 How are microbes affected by pH?
1. Microbial enzymes can be denatured due to pH change
2. pH may affect the solubility of other chemicals --- which may
become toxic to microbes at high concentrations or may be
limiting at very low concentrations
5. Proper Competing Organisms: Microbes are particular to the types of organisms
that are around them. To be able to survive, they must be able to compete or
have a favorable association with the microbes around them.
6. Aeration: The need of presence or absence of oxygen.
 aerobic – requires oxygen to survive
 anaerobic – can survive or survives better in the absence of oxygen

Beneficial Activities of Soil Organisms

1. Decomposition of organic materials

2. Nutrient transformation
3. Weathering reactions/ Soil formation
4. Treatment of wastes
5. Improve soil physical properties
Decomposition: microbially-mediated process whereby complex organic matter are
reduced to simpler ones.

1. This is driven by enzymatic reactions involving different soil

microorganisms. Decomposition is efficient under aerobic conditions.
CH 2O + O2 ====> CO2 + CH2O + energy.
 Decomposition can still proceed under anaerobic
condition but is relatively less efficient than
decomposition under anaerobic conditions.
2. All stages of decomposition are present in soils.
- Rate of decomposition is largely determined by the composition of the
organic matter/organic residue. Organic residues with high content of
recalcitrant substances (such as lignin and chitin) and has a wide C/N
ratio are usually harder to decompose.

Nutrient Transformation

1. Microbes are important in biochemical processes involving the

transformation of nutrients. These transformation reactions may be of
agricultural or environmental importance.
2. Transformations that are agriculturally relevant:
Examples:

Nitrification - conversion of ammonium (NH4+) to nitrate (NO3-) by two

bacteria.

Two-step process

2 NH4+ + O2 ===> 2 NO2- + 2 H2O + 4 H+ + energy ------ done by

Nitrosamines sp.

2NO2- + O2 ===> 2 NO3- + energy ------done by Nitrobacter sp.

Nitrogen Fixation – conversion of Atmospheric nitrogen (N2) to ammonia

N2 ===> NH3 ------ done by Rhizobium sp in nodules in roots of
legumes.

3. Transformations that are environmentally relevant.

Example:

Denitrification - conversion of nitrate (NO3-) to NO, N2O and primarily to

N2 (nitrogen gas) – done my denitrifiers/ denitrifying microbes
 Weathering Reactions/ Soil Formation

1. Microorganisms produce acidic exudates which can contribute to

solubilization of the parent materials.
2. Cyanobacteria, algae and lichens are considered pioneer organisms in soil
formation because of their dual roles in acquiring carbon and nitrogen from
the atmosphere. Carbon and nitrogen are two essential elements that are
lacking in the soil parent material.

Treatment of Waste
1. Nitrate from septic systems, for example can be denitrified by denitrifying
organisms.
2. Industrial wastes such as PCE or TCE (can cause cancer) and pesticides may
be degraded via microbially-mediated reactions.

Improve Soil Physical Properties

1. Fungal hyphae may wrap soil particles encouraging the production of
aggregates
2. Mucilaginous exudates of some bacteria may serve as “glue” in aggregate
formation

Metabolic Classification of Microorganisms:

1. Based on Energy Source:

a) Phototrophic – microbes that use light as their primary source of energy

b) Chemotrophic – microbes that use chemical compounds and reactions as
their source of energy

2. Based on Carbon Source:

a) Heterotrophs - microbes that obtain carbon from organic compounds ;

most numerous type
b) Autotrophs: Obtains carbon (C) from by fixation of CO 2

Soil Organic Matter (SOM)

Definition: living or dead plant or animal material in soil. Ranges from large undecomposed
material to fine, highly decomposed material.

Humus: stable fraction of organic matter in the soil.

 complex organic materials that is resistant to further decomposition.

 Composition of SOM

1. Green tissue - 85 to 90% water and 10 to 15% dry matter.

2. Dry Matter
a) C, H. and O - 90%.
b) Contains all nutrients but important reservoir of N, P, K, S.
c) Rapidly decomposing materials - cellulose, starches, sugars,
amino acids and proteins.
d) Slowly decomposing materials - fats, oils, resins, and lignin.
e) C/N ratio – ratio of C to N in the plant residue (e.g. rice straw,
peanut shoots)

Decomposition : microbially-mediated process

Relation of C/N ratio in organic materials to decomposition and soil N.

1. Wide ratio (> 30) - material low in N so microbes lack N and decomposition
is slow. If any soil N is present in the soil, microbes will compete with plants
for it.
 Have to apply additional N to hasten decomposition of wide C/N
material and prevent N deficiency on crop.
2. Intermediate ratio (15 to 30) - balanced N content. Meets microbe’s needs
and does not cause N deficiency.
3. Low ratio (< 15) e.g. legume residues- contains excess N and residues is fast.
Nitrogen will be released into the soil with decomposition. Basis for legumes
in rotations or green manure crops.

Function of Organic Matter in the Soil

1. Source of essential elements.

 Other than those provided by fertilizers, organic matter is the major
source of nitrogen in most soil systems.
 Amount and type of nutrients in organic materials depends on the
type of organic residues
2. Substrate of most soil organisms.
 Source of C and energy of most microorganism
(chemoheterotrophs).
3. Provides the distinct black color of soils that improve the soils ability to absorb
the sun’s heat energy
4. Improves soil physical properties
 A good cementing agent that contributes to structure development
via aggregate formation and stabilization
 Improvements in structure contributes to improvement in soil and
water movement through the soil body
5. Contributes to CEC
  Exposed functional groups in organic materials (e.g., carboxyl and
amino groups) contribute to the net negative charge of the soil, and
hence to the CEC of the soil.
6. Good buffer against pH change
 Exposed functional groups may protonate or deprotonate in
response to a change the chemistry of the soil solution and thus
may serve as buffer against drastic change in soil pH.

Review Questions:
1. What organisms comprise the soil macrofauna?
2. What organisms comprise the soil microfauna? Soil microflora?
3. Familiarize the properties of each group of soil organisms
4. What is mycorrhiza? What are lichens?
5. What is the relationship of organism size to population density?
6. What is the general distribution of organisms with depth in a soil profile?
7. What are the factors affective microbial growth and survival?
8. What are the beneficial effects of soil microorganisms?
9. How do you classify soil microbes according to their energy source? According to their
carbon source?
10. Define soil organisms?
11. What is humus?
12. What is the relationship of decomposition rate to C/N ratio?
13. What are functions of organic matter in soils?