Module 6 Soil Biology and Organic Matter

Lesson 1

Soil Biology

……………………………………………………………………………………………
Objectives Introduction
……………………
At the end of this lesson, you
are expected to: Soil properties are strongly influenced by the
activity of the organisms that inhabit the soil. In
Understand the
importance of soil
this lesson you will learn the macro and
biological properties in microorganisms that inhabit the soil and their
agriculture and the roles in the proper functioning of a healthy
environment
agricultural soil.
Key Concepts
a. Macrofauna
b. Microfauna
c. Microflora
d. Decomposition
e. Phototrophic
f. Chemotrphic
g. Heterotrophs
h. Autotrophs

Section 6.1
1.1
Soils are Alive!

In this activity, we will observe the organisms that is found

on and underneath its surface.

Procedure
 Go outside and shovel approximately 6inches deep
from the soil surface
 Observe any organisms in the exposed soil
 Get a clod from the shoveled soil and smell if there
is any.
Analysis
 What part of the soil the macro organisms are
mostly found? And what could be the reason of
them flourishing on that particular portion of the
soil
 Does the soil produce a distinct smell? What could
be the reason for it?

Soil Biology and Organic Matter| PAGE \* MERGEFORMAT 59

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 – 108 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)

Soil Biology and Organic Matter| PAGE \* MERGEFORMAT 59

  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, lignin’s and complex organic compounds
 Usually multicellular but may include unicellular organisms
(yeast)

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

fungus colonizes 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)

Population
density
Microbial Group Example Size (µm)
(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

Soil Biology and Organic Matter| PAGE \* MERGEFORMAT 59

 Thousands of organisms per gram soil
Depth Aerobic Anaerobic Actinomycetes Fungi Algae
(cm) 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
is reduced to simpler ones.

Soil Biology and Organic Matter| PAGE \* MERGEFORMAT 59

 1. This is driven by enzymatic reactions involving different soil
microorganisms. Decomposition is efficient under aerobic conditions.
CH2O + 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

Nitrosomonas 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

Soil Biology and Organic Matter| PAGE \* MERGEFORMAT 59

 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 CO2

Soil Biology and Organic Matter| PAGE \* MERGEFORMAT 59

 ………………………………………………………………………………………………………………………………………………

Section 6.2 Application

Knowing the Biology of our Soil

Think as if you are the 1. What organisms comprise the soil
one in-charge of the macrofauna?
soybean farm 2. What organisms comprise the soil
microfauna? Soil microflora?
3. Familiarize the properties of each
Scenario: group of soil organisms
4. What is mycorrhiza? What are
The soybean farm needs to have a lichens?
fertilization program. As the one in 5. What is the relationship of
charge for the fertilization organism size to population
program, you are asked to purchase density?
the needed fertilizers (N,P,K). 6. What is the general distribution of
organisms with depth in a soil
11. Rank these fertilizers in terms profile?
of the amount that the farm will
7. What are the factors affective
be needing (1 being the highest
microbial growth and survival?
amount and 3 the lowest). What
is the main reason for your 8. What are the beneficial effects of
ranking? soil microorganisms?
9. How do you classify soil microbes
according to their energy source?
According to their carbon source?
10. Define soil organisms?

References

Brady, N.C. and Weil, R. R. 2017. The Nature and Properties of Soils, 15th edition. Pearson
Education Limited, Edinburgh Gate, Harlow, Essex CM20 2JE, England, 1105 pp.

Recommended Website to Explore

https://soilhealthinstitute.org/

Soil Biology and Organic Matter| PAGE \* MERGEFORMAT 59