Chapter 5

SOIL ORGANISMS AND ORGANIC MATTER

Introduction

Soil organisms are creature that spend all or part of their lives in the soil environment.
Every handful of soil is likely to contain billions of organisms, with representatives of nearly every
phylum of living things. Living organisms and dead organic matter in soils are constantly changing.
Soil organisms mix and aerate soil, fix atmospheric N 2, decompose dead organic substances,
oxidize many elements and recycle nutrients.
Fungi and bacteria are the most important organic matter decomposers. Both fungi and
bacteria form symbiotic relationships in which two different organisms live in association, with
both benefiting. Certain bacteria called autotrophs get their energy from oxidizing important soil
elements, including nitrogen, sulfur, iron, manganese, and carbon monoxide. Some algae fix
atmospheric nitrogen and become part of the organic matter. Actinomycetes help in the
decomposition of organic materials. Protozoa are also decomposers and act as ppredators on
bacteria.

5.1 Kinds of Soil Organisms

5.1.1 Macroorganisms in the soil

1. Kingdom Animalia (formerly Macrofaunae)

- The large animal life- that inhabit the soil range in size from large burrowing animals
such as rabbits down to mites which are barely visible to the eye
- Subsisting largely on plant materials (small mammals- mice, squirrels); insects— ants,
beetles, grubs, etc.; millipedes; mites; snails; earthworms

2. Kingdom Plantae: Plants

- obtain energy from the sun and can exist as stationary life
1) Macroplantae (Macroflora) - plant roots systems

3. Fungi: Molds, mushrooms, yeasts

- Without ability to the sun for energy; they live on dead or living plant or animal tissue
- fungi are a curious assortment of one-celled organisms (yeasts) to multi-cellular
filamentous molds and mushrooms

5.1.2 Microorganisms in the soil

1. Kingdom Protista - protozoans

– unicellular, most numerous; ingest bacteria, fungi, other microbes, nematode larvae and
eggs and even smaller protozoa

2. Microplantae (Microflora) – algae

- microscopic organism that carry on photosynthesis
- the main groups are green algae, yellow-green algae and diatoms
- not important as decomposers of organic matter but are producers of new photosynthetic
growth

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 3. Kingdom Monera – bacteria and actinomycetes
- decompose organic matter
- actinomycetes are not as effective as bacteria and fungi in decomposing organic
substrates

Relative number and biomass of soil flora and fauna found in soils (values common in surface
soils at 15 cm)
--------------------------------------------------------------------------------------------------------
Microorganisms No./ m2 No./g Biomass/ kg/ha
_______________________________________________________________
Microflora
Bacteria 1013 - 1014 108 - 109 400 - 5,000
12 13
Actinomycetes 10 - 10 107 - 108 400 - 5,000
Fungi 1010 - 1011 105 - 106 1,500 - 15,000
Algae 109 - 1010 104 - 105 1 - 500
Microfauna
Protozoa 109 - 1010 104 - 105 20 - 200
6 7
Nematoda 10 - 10 10 - 102 10 - 150
Other fauna 102 - 104 10 - 100
Earthworms 10 - 103 100 - 1,500
________________________________________________________________

5.2 Bacteria
- Single-cell; prokaryotic organisms.
- Multiply rapidly by elongating and dividing into two parts
- Bacteria are very small-seldom exceeding 4 to 5 microns (0.004 to 0.005 mm) in length,
- Shape of bacteria varied from nearly round, rod-like, or spiral; rod shape seems to
predominate in the soil
- Motile, swimming about in the soil water by means of hair-like cilia or flagella
- Population- few billion to more than a trillion/g soil; biomass of 400-5,000 kg/ha live weight
is commonly found in a plow layer of fertile soils

Azotobacter

a) Rhizobium b) Azospirillum c) Cyanobacteria

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 d) Pseudomonas marginalis

Figure 5.1. Examples of bacteria: a) Rhizobium, b) Azospirillum, c) Cyanobacteria, and d)

Pseudomonas marginalis

Classification of Bacteria according to oxygen requirements

1. Aerobic – bacteria that thrive only in the presence of free oxygen.
2. Anaerobic – bacteria that can live even in the complete absence of oxygen (as in paddy
or poorly drained soils).
3. Facultative – bacteria that can grow in the presence or absence of free oxygen.

Classification of Bacteria according to Energy and Carbon Requirements

1. Autotrophic – uses CO2 as source of C
- carbon source- CO2
- energy source- oxidation of simple inorganic compounds e.g. (NH4+, H2S, Fe2+)

(a) Chemoautotrophic – use inorganic chemical compounds as source of energy

(b) photoautotrophic – use sunlight as source of energy.

2. Heterotrophic – oxidizes organic matter for carbon and energy.

Classification of Bacteria according to temperature for optimum activity

1. Psychrophilic - <20oC
2. Mesophilic – 25oC – 35oC
3. Thermophilic– 45oC– 65oC
Example 1. Pseudomonas
- most aerobic except denitrifying species
- feed on sugars, amino acids, alcohols, aldose sugars, hydrocarbons, oils, humic acids
- produce diffusible fluorescent pigments
- pathogens - will producing cellulases and pectinases
- plant-growth promoting (ethylene, auxins)
Example 2. Cyanobacteria
- Obligate phototrophs with aerobic photosynthesis
- Formerly classified as algae but shifted to bacteria
- Forms range from unicellular, colonial, filamentous heterocystous and filamentous
branching
- Capable of N fixation in heterocysts

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5.3 Actinomycetes

- Resemble molds- filamentous and produce fruiting bodies

- Mycelial threads-smaller than fungi.
- Unicellular; about the same diameter of bacteria; both are prokaryotic; referred to as mold-
like bacteria
- Simplify complex and resistant organic compounds (cellulose chitin and phospholipids).
- Aerobic heterotrophs that live on decaying organic matter in the soil
- Only few species are motile
- Many species produce antibiotic compounds that kill other microorganisms (e.g.
Actinomycin, Neomycin and Streptomycin)
- tolerate low nutrient, alkaline, dry soil

Figure 5.2. Examples of actinomycetes a) Streptomyces b) Different species of actinomycetes

5.4 Fungi
- No chlorophyll and use organic matter for energy and carbon (chemoorganotrophs)
- Vegetative form-usually thread-like and filamentous.
- Mycelial threads-simple and restricted or profusely branched.
- Have plant-like eukaryotic cells with a nuclear membrane and cellwalls; but unlike other
plants, have no capability for photosynthesis
- Reproduce naturally by means of spores with few exceptions - most part of fungi is
potentially capable of growth
- Include microscopic yeasts, mushroom and bracket fungi
- aerobic- although some can tolerate the rather low O2 concentrations and higher level of
CO2 found in wet or compacted soils
- Fungi thrive-extremes of soil acidity and alkalinity.
- Effective decomposers of resistant organic compounds (lignins, cellulose and gums).
- Mycorrhizae-association between fungi and plant roots; help in solubilization of
phosphorus and its absorption.

a) Penicillium b) Aspergilus flavus c) yeasts

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 d) Molds e) Ganoderma

Figure 5.3 Examples of fungi

5.5 Soil Algae

- Chrolorophyll-bearing organisms, and like higher plants, are capable of performing

photosynthesis.
- Obtain energy from organic matter.
- Cells are either prokaryotic or eukaryotic;
- Groups of algae (blue-green, green and diatoms).
- Add organic matter in soil and also fix atmospheric nitrogen.
- Blue-green algae (BGA) fix atmospheric N; red algae, azollae and brown sea weeds are
used as fertilizers
- Alga as food (Posphyra); agar for stiffening food; Chlorella and Nostoc commone as
human food

a) Blue green algae b) diatoms c) Nostoc commune

Figure 5.4. Examples of algae

5.6 Beneficial activities of soil organisms

5.6.1 Decomposition of organic material

The death of organisms eventually results in the rupture of cell membranes and the
expulsion of many soluble cell substances into the soil and water solution. The organic solids
(most of the non-water portion of a dead organism) are altered only very slowly until
microorganisms attack them. The decomposing organisms excrete a variety of enzymes to begin
breakdown of the materials. The decomposition rate is directly proportional to the number of
microbes present. Microbes absorb the nutrients released during decomposition- particularly
nitrogen and carbon- and use them for their growth and reproduction.

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Rate of decomposition

1. Sugar, starches, and simple proteins rapidly decomposed

2. Crude proteins
3. Hemicelluloses
4. Cellulose - very slowly decomposed
5. Lignins, fats, waxes, etc.

When organic tissue is added to soil, three general reactions take place:

- The bulk of the material undergoes enzymatic oxidation with CO2, H2O, and heat as the
major products.
- The essential elements N, P, and S are released and/or immobilized.
- Humus - compounds resistant to microbial action are formed

5.6.2 Transformation of nutrients (Sulfur and Phosphorus)

1. Sulfur Transformation
- Organic sulfur constitutes more than 90% of the total sulfur present in most surface soils
- Inorganic form account for less than 25% of the total sulfur in most agricultural soils
- Microbiologically mediated transformations:
 Oxidation and reduction reactions
 Mineralization and immobilization reactions
 Volatilization reactions

a. Microbial oxidation of inorganic S compounds

- mediated by chemoautotrophic and chemoheterotrophic microorganisms

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 Figure 5.5. The Sulfur Cycle

Sulfur oxidizers:
a. Thiobacillus sp. - unicellular; chemoautotrophs
b. Purple and green sulfur bacteria - Phototrophs
c. Include wide range of chemoheterotrophic bacteria actinomycetes and fungi
d. Arthrobacter, Bacillus, Micrococcus, and Pseudomonas-other heterotrophic bacteria
e. Other sulfur bacteria
▪ Beggiatoa,

▪ Chromatium, and Chlorobium – in rice paddy (anaerobic)

b. Microbial sulfate reduction

- reduction of SO4-2 to H2S is mediated mainly by anaerobic sulfate reducing bacteria
Desulfovibrio sp.
Desulfomonas sp.
Desulfotomaculum
- important in waterlogged soils; reaction is strictly anaerobic
- sulfate-reducing bacteria are a major cause of corrosion of underground iron pipes; can
produce a black layer by using the organic matter in root exudates to reduce soil sulfates
to ferrous sulfides

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2. Phosphorus Transformations
- the primary mineral form of phosphorus is rock phosphate, or apatite
- the total amount of organic P in a soil is usually strongly correlated with total organic
carbon
- Biological P transformations includes:
 Mineralization and immobilization
 Redox reactions
 Solubilization

a. Mineralization and immobilization of P

- Phosphorus mineralization is an enzymatic process
- Phosphatases catalyze a variety of reactions that release phosphate from organic
P compounds to the soil
- Once P is mineralized, it can be taken up by plants or immobilized back into
microbial cells, or it can form insoluble inorganic complexes
- If more P are present in the residue than is needed for C assimilation, net
mineralization of orthosphosphate ions occur
- C:P ratio < 200:1 results in mineralization
- C:P ratio > 300:1 results in immobilization

Figure 5.6. The Phosphorus Cycle

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 Reactions involved:

Figure 5.7. P reactions in the soil.

- Inorganic P minerals are generally found as Al and Fe phosphates in acidic soils while Ca
phosphates dominate in alkaline soils
- plant roots and microorganisms can enhance the dissolution of P compounds by the
release of CO2 and organic acids in the soil solution
- H2CO3 can promote the acid dissolution of Ca and Mg phosphate compounds
- The acidity produces by the nitrifying bacteria and sulfur oxidizing bacteria promotes
solubilization of insoluble phosphate salts

5.6.3 Promoting soil aggregation through by-products of their activities

Humus tends to give surface horizons dark brown to black colors. Granulation and
aggregate stability are encouraged, especially by the non-humic substances produced
during decomposition. The humic fractions help reduce the plasticity, cohesion, and
stickiness of clay soil making these soils easier to manipulate.

5.6.4 Biological Nitrogen fixation: symbiotic, non-symbiotic, associative

- the atmosphere contains 78% N2

- Biological conversion of inert dinitrogen gas of the atmosphere (N 2) to nitrogen-containing
organic compounds or to forms readily utilize in biological processes

- Diazotrophs – N-fixing bacteria

- the site of N2 reduction is the enzyme nitrogenase
- leghemoglobin gives active nodules a red interior color
- 45 x 106 Mg N/yr (45 t N/yr) fixed in meadows and grasslands

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1. Symbiotic N-fixation
- the association involves an N2-fixing prokaryotic microsymbiont (e.g. Rhizobium,
Kleibsiella, Nostoc, or Frankia) and a photosynthetic host (e.g. leguminous or non-
leguminous plant or water fern)

Classification of Rhizobia bacteria:

a. Rhizobium - fast growing, acid-producing
b. Bradyrhizobium- slow growers; do not produce acids
c. Azorhizobium- produces stem nodules

The infection process:

a. Infection
- penetration of root hairs and formation of infection threads
- entry via wounds or sites of lateral root emergence
- penetration of root primordia
b. nodule development
- as the infection thread penetrates the root cortex and the Rhizobia it contains
are released into host cells, cell division and enlargement of these cells results

Figure 5.8. The infection process of legume roots by Rhizobia bacteria.

b. Associative
– N2 fixation by microorganisms associated with grasses, sugarcane and cereals ex.
Azospirillum

c. Nonsymbiotic N2 fixation
- free-living N2 fixation; organisms are not directly associated with higher plant
ex. Azotobacter – temperate; neutral to alkaline soils
Beijerinckia - tropical soils
Clostridium - anaerobic condition
Cyanobacteria -aquatic environments
Blue-green algae and Nostoc

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5.6.5 Phosphorus solubilization (mycorrhiza)

1. Solubilization of Inorganic P
 A wide range of organic acids is produced by microorganisms and plants and may
act as chelating agents to solubilize Al, Fe, Ca, and Mg phosphates, resulting to the
release of orthophosphate into the soil solution
 P- solubilizing bacteria
ex. Bacillus megatherium
Bacillus pumillis
Thiobacillus thiooxidans
species of Pseudomonas and Arthrobacter

 P- solubilizing fungus - ex. Aspergillus niger

 P- solubilizing organisms are able to replace 50% to 70% of phosphorus input in the
soil

2. Mycorrhizal associations
▪ Mycorrhiza- means fungus-root; applied to fungus-tree associations
Types of mycorrhizae:
a. Ectomycorrhiza- presence of hyphae between root cortical cells; forms a mantle of
fungal tissue that may completely cover the feeder roots called the Hartig net; ex.
Agaricus
- host is gymnosperm (e.g. Pine)

b. Endomycorrhiza- the fungus grows within cortical cells; infect most agricultural
crops; ex. Glomus, Gigaspora

Role of mycorrhizae in plant nutrition:

- improve overall plant growth by improving P and Zn nutrition
- allow more efficient use of P and Zn in fertilizer
- stimulate N2 fixation in nodulated plants by increasing P flow through plant roots
- increase disease tolerance in plants by improving the plant nutrition and by
competing with pathogenic microorganisms for space on the plant root
- immobile some heavy metals such as Zn, Cd, and Mn
- Improve water use and drought tolerance
- improve soil structure by binding soil aggregates together

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 Figure 5.9. Mycorrhizal association in plants

5.6.6 Other beneficial activities

1. Pesticide degradation
 pesticides are chemicals designed for the control of pest populations
 The duration of effectiveness of a pesticide (persistence) is governed by the
chemical structure and environmental conditions
 how long a pesticide persists in soil reflects the time that the pest will be subject to
control
 Persistent pesticides may:
- Adhere to edible portions of root crops
- Be assimilated by plants and accumulate in edible portions
- Transported with eroding soil particles to nearby waterways

Types of pesticide metabolism:

a. Detoxication- conversion of a molecule inhibitory in the concentration used to a

nontoxic product
b. Degradation – the transformation of a complex substrate into simple products
c. Conjugation, complex formation, or addition reactions - an organism makes the
substrate more complex or combines the pesticide with cell metabolites; often are
detoxifications
d. Activation - conversion of nontoxic substrate into a toxic molecule
e. Defusing- conversion of a nontoxic molecule which is subject to enzymatic
activation, to a nontoxic product that no longer is subject to activation

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 Heterotrophs which use pesticides as substrates:

a. Species of Agrobacterium, Arthrobacter, Bacillus, Clostridium, Corynebacterium,

Flavobacterium, Kleibsiella, Pseudomonas, and Xanthomonas
b. Fungi – Alternaria, Aspergillus, Cladosporium, Fusarium, Glomerella, Mucor,
Penicillium, Rhizoctonia, Trichoderma
c. Actinomycetes- Micromonosphora, Nocardia and Streptomyces

It is rarely possible to predict which species or even which genus is responsible for a
particular transformation in nature.

2. Production of growth-promoting hormones

- enhance plant growth (IAA, GA, cytokinins)

e.g. Azospirillum brasilense – mainly for N2 fixation, but principally a source of plant
hormone, IAA
Pseudomonas sp. – another source of IAA
Yeasts group series – produce vitamins and growth hormones

3. Remediation of oil and other xenobiotics

e.g. Pseudomonas sp.

4. Biocontrol – competition and /or suppression, direct antagonism, produce antibiotics

a) Agrobacterium for the control of crown gall in grapes and other horticultural crops
b) Bacillus sp- for both root-rot and insect control
c) Pseudomonas sp. – for biocontrol of root disease via Fe sequestering or antibiotic
production
d) Trichoderma sp. - for biocontrol via cellulase or chitinase

Figure 5.10. Trichoderma on a tree bark (a) and hyphal structure on a microscope (b).

5. Production of antibiotics

– to suppress growth of other microorganisms; increase plant resistance towards

harsh conditions and diseases (Actinomyces series)
e.g. Streptomycetes – actinomycete producing the antiobiotic known as
Streptomycin
Actinomyces microflavus – antibiotic-producing bacteria
Bacillus sp and Pseudomonas sp- some strains in these genus is Plant
Growth Promoting Rhizobacteria (PGPR)
Pseudomonas – liberate procyanin and related compounds

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 Fungi:
Penicillium – Penicillin Aspergillus
Fusarium Trichoderma

6. Potassium- solubilizing bacteria

- also known as silicate bacteria; could decompose potassium minerals into soluble
potassium ions
e.g. Bacillus mucilaginosus, Bacillus circulans, and Bacillus macerans

5.7 Composition of organic matter: Carbohydrates, proteins, lignins, fats, waxes, tannins
Tissues of a given plant differ considerably in their makeup. Carbohydrates which
range in complexity from simple sugars and starches to cellulose, are usually the most
plentiful of plant organic compounds.
Lignins, which are complex compounds with multiple ring-type or phenol
structures, are components of plant cell walls. The content of lignin increases as plants
mature and is especially high in woody tissues. Other polyphenols such as tannins may
comprise as much as 6 or 7% of the leaves and bark of certain plants. Lignins and
polyphenols are notoriously resistant to decomposition. Certain plant parts, especially
seed and leaf coatings, contain significant amount of fats, waxes and oils, which are more
complex than carbohydrates, but less so than lignins.
Proteins contain about 16% nitrogen and smaller amounts of other essential
elements, such as sulfur, manganese, copper, and iron. Simple proteins decompose and
release their nitrogen easily, while complex crude proteins are more resistant to
breakdown.

5.8 Types of organic matter decomposition

1. Aerobic OM decomposition
- When organic tissue is added to an aerobic soil, three general reactions take place:
a) Carbon compounds are enzymatically oxidized to produce carbon dioxide,
water, energy, and decomposer biomass.
b) The essential nutrient elements such as nitrogen, phosphorus, and sulfur
are released and/or immobilized by a series of specific reactions that are
relatively unique for each element
c) Compounds very resistant to microbial action are formed, either through
modification of compounds in the original tissue or by microbial synthesis

- OM undergoes enzymatic oxidation by soil organisms under aerobic conditions

with CO2, heat or energy and water as the major products:

2. Anaerobic OM decomposition

- The products of anaerobic decomposition include a wide variety of partially

oxidized inorganic compounds, such as organic acids, alcohols, and methane gas.
Anaerobic decomposition releases relatively little energy for the organisms
involved; therefore, the end products still contain much energy.

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 - In poorly drained conditions decomposition of organic matter is done by anaerobic
organisms
- the process is much slower and the products include methane (CH 4), hydrogen
sulfide (H2S), S, H2, and organic acids.

C:N Ratios

 Bacteria require about 5 grams of carbon for each gram of nitrogen assimilated or
used
 C:N in a ratio of 5:1.
 Decomposing microorganisms have first priority for any mineralized N.
 This use of N by decomposers results in insufficient N for plants.
 Eventually period of N starvation is over after all the high C:N material is
decomposed.

Carbon-nitrogen ratio (C:N ratio) of organic matter

C = C content (Optimum for faster decomposition <20/1)

N N content

 affects rate of decay – high C:N slow decomposition

 affect N-mineralization- high C:N cause temporary N- fixation

_________________________________________________
Material C :N
Soil OM (humus) 10-12 : 1
Bark of trees 200 : 1
Rice straw 50 : 1
Corn stover 55 : 1
Sugarcane trash 116 : 1
Poultry manure 6.7 : 1
Cattle manure 16 : 1
Swine manure 8.4 : 1
_________________________________________________

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 Functions of Humus:

 holds water and nutrients;

 it sticks together and helps establish and maintain a strong crumb structure and
thus reduce soil erosion
 it provides some nutrients (N & P) as it is slowly decayed by microbial activity,
 buffers effects of pesticides
 humus decomposes at the rate of 2.5% per year

5.9 Nitrogen transformations: The N Cycle

- The total mineralizable N in soil depends on its original organic N content
- The total N depends on climate, vegetation, topography, age and soil management
- Soil N decreases as the average soil temperature increases (for every 10 0C rise in mean
average soil temperature, the amount of soil N is two to three times lower)
- The optimum temp for mineralization is between 40-600C
- The optimum water content for mineralization is between 50-70% water-holding capacity
- There is more soil N under permanent grass vegetation than there is under forest soils.
- Cultivation invariably reduces the soil N content; no tillage soil has higher soil N levels
than does a tilled soil
- Predominant forms of organic N in soils are proteins, nucleic acids chitin, peptidoglycan
and amino sugars; bacteria are about 50% protein

Figure 5.11. The Nitrogen Cycle

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1. Mineralization
- biological conversion of organic nitrogen (bounded in organic matter as proteins or
nucleic acids, amino acids, etc.) into inorganic nitrogen available for plant use. The
microbiological processes involved are ammonification and nitrification.

2. Nitrification
- microbial oxidation of ammonium (NH4+) - N into nitrite (NO2-) and nitrate (NO3-).

2 types of Nitrification:

a. Chemoautotrophic Nitrification – performed by gram (-) chemoautotrophic nitrifiers

belonging to the family Nitrobacteriaceae

- dominant process in the neutral to alkaline soils and is perhaps 100 to 1,000 times
faster than heterotrophic nitrification

2 Nitrifier groups:

a. Ammonium oxidizers (NH4+ to NO2-) - prefix (Nitroso)

b. Nitrite oxidizers (NO2- to NO3-) – prefix (Nitro)
Nitrobacter,
Nitrococcus,
Nitrospina

b. Heterotrophic Nitrification
- formation of NO2- and NO3- from NH4+, NO2- and organic N by heterotrophic
organisms
- heterotrophic nitrifiers are both bacteria and fungi; representative bacteria examples
are:
Nitrosomonas, Nitrosolobus,
Nitrosospira, Nitrosovibrio
Nitrosococcus Pseudomonas
Arthrobacter, Aerobacter,
Mycobacterium, Streptomyces,
- fungi examples: Aspergillus and Penicillium

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3. Immobilization
- conversion of inorganic nitrogen (NH4+ or NO3-) back to organic nitrogen.
- also synonymous to assimilation
- the N is immobilized with respect to plants; if it is being turned into microbial cells, it
cannot be taken up by plants until those microbial cells decompose or mineralize

4. Denitrification

- reduction of nitrate-N to gaseous N by facultative anaerobic soil organisms.

▪ When NO3- in the thin aerobic surface of paddy soils is leached down to the reduced
subsoil, the facultative bacteria, Denitrificans reduce the NO3- to nitrite and then to
gaseous nitrogen forms, nitrous oxide (NO). The general form of reaction is as follows:

Figure 5.12. Role of bacteria in the nitrogen nutrition of plants.

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