A Strong Partner for Sustainable Development

Module
in
SOILS 101

PRINCIPLE OF SOIL SCIENCE

College of CAFES
BSA
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Module No. _5_

SOIL ORGANISMS AND ORGANIC MATTER

Topic

2ND Semester AY 2020-2021

VIMBEE A. ERESUELA
Instructor 1

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TABLE OF CONTENTS
Page
Cover page 1
Title Page 2
Table of Contents 3
Instruction to the Users 4
Introduction 5
Chapter

Title of the Chapter 6

Overview 6
Learning outcomes 6
Pre-test 6

Time Allotment 7
What is colloids? 7
Examples of the silicate and non-silicate clay minerals 8
commonly occurring in soils
How Organic Colloids contribute to the chemical properties 12
of the soil?
Factors affecting the adsorption of cations in soils 12
The Concept of Cation Exchange Capacity 13
What is Percentage Base Saturation (%BS) and how it is 18
calculated?
How sodic soil are reclaimed and calculated? 19
What is soil pH? 21
What is lime? 24
Saline and Sodic soils and its characteristics 27
Activities/Exercises 29
Evaluation/Post-test 29
References 31
Greetings and Students information & Privacy Notice 32
Back Cover (WPU-Vision 2020, Mission and Core Values) 33

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INSTRUCTION TO THE USER

This module would provide you an educational experience while

independently accomplishing the task at your own pace or time. It aims as
well to ensure that learning is unhampered by health and other challenges. It
covers the topic about the Biological Properties of the Soil.
Reminders in using this module:

1. Keep this material neat and intact.

2. Answer the pretest first to measure what you know and what to be
learned about the topic discussed in this module.
3. Accomplish the activities and exercises as aids and reinforcement for
better understanding of the lessons.
4. Answer the post-test to evaluate your learning.
5. Do not take pictures in any parts of this module nor post it to social
media platforms.
6. Value this module for your own learning by heartily and honestly
answering and doing the exercises and activities. Time and effort were
spent in the preparation in order that learning will still continue amidst
this Covid-19 pandemic.
7. Observe health protocols: wear mask, sanitize and maintain physical
distancing.

Hi! I’m Blue Bee, your WPU Mascot.

Welcome to Western Philippines University!

Shape your dreams with quality learning experience.

STAY SAFE AND HEALTHY!

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INTRODUCTION

This module will serve as an alternative learning material to usual way of

classroom teaching and learning delivery. The instructor will facilitate and explain the

module to the students to achieve its expected learning outcomes, activities and to

ensure that they will learn amidst of pandemic.

This module is about the Soil organisms and organic matter as soil organisms, the chief

roles of microorganisms, beneficial effect of soil microorganisms, biological nitrogen

fixation and soil organic matter. This module is comprised as well of pre-tests,

exercises and post-tests that you can answer at your most convenient time and place.

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Chapter 5

SOIL ORGANISMS AND ORGANIC MATTER

Overview

Module 5 covers the topic about the Biological properties of the soil. A healthy soil
teems with immense community of living organisms. Through their role in the
decomposition cycle, they regulate the flow of energy through the soil, the cycling of
nutrients, and the productivity of agroecosystems. Soil organisms span a wide range
in size, from microscopic forms such as bacteria, fungi, and protozoa, large animals
such as insects, worms and burrowing mammals.,

At the end of this module, you can:

• Identify the different soil organisms and their beneficial role

in soil;
• Explain the biological nitrogen fixation and other processes;
• Define soil organic matter, composts and composting; and
• Enumerate the factors that affect decomposition

Pre-test
Directions: To start off, you have to answer the pre-test for you to measure how
much you know about the topic. You can start now. Each question has ONLY ONE
CORRECT ANSWER. Choose the one you believe to be best. Each question is worth 1
point. Read each question fully and carefully take your time. GOD BLESS!
Test 1. Multiple Choice. Choose the letter of the correct answer.
1. The original source of most organic matter in soil is?
a. plant residues
b. bodies of dead animals and insects
c. soil inhabiting microorganisms
d. rocks
2. Association between plant root and fungi is known as?
a. Lichen c. Competition
b. Symbiosis d. Mycorrhiza
3. Rhizobium-legume association is an example of?
a. Mutualism c. Predation
b. Neutralism d. Symbiosis
4. Microorganisms that are most active in the decay of organic substances in soils
are?
a. Autotrophs c. Anaerobes
b. Aerobes d. Phototrophs
5. Nitrogen is the most limiting element in crop production, except for legumes. The
available form of nitrogen is?
a. Organic matter c. Ammonium
b. Nitrate d. Both b and c

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6. The enzyme responsible in nitrogen fixation?

a. nitrate reductase c. nitrogenase
b. catalase d. carboxylase
7. The conversion of ammonium (NH4) into organic N?
a. immobilization c. mineralization
b. nitrification d. denitrification
8. Of the following, the one that is not carbohydrate is?
a. Lignin c. Cellulose
b. Starch d. Hemicellulose
9. Product of nitrification is?
a. N2 b. NO3 c. NH4 d. N2O
10. Product of denitrification?
a. N2 c. NH4
b. NO3 d. NH3

B. Time Allotment: 5 hours

C. Discussion

Soil Organism that affects soil Properties

Soil organism are composed of large and small plants and animals. The larger
ones consist of insects, worms, moles, etc. and the smaller ones include bacteria,
fungi, actinomycetes, algae, nematodes and protozoa. The larger organisms primarily
prepare organic materials for further degradation by breaking them into smaller
pieces. The smaller organisms cause biochemical changes into organic materials

Role of larger soil organisms – assist in the decomposition by ingesting

plant residues, breaking them into particles, and mixing them as waste throughout the
moist soil environment. These wastes become food for the microorganisms, which
digest the organic matter, releasing plant nutrients and gases, and producing glues
that stick the soil mineral particles together to form aggregates. The larger organisms
also influence soils mainly by being mixers of soil materials.

Soil macroorganisms

Worms

• may deposit 10-15 tons of wormcasts per acre per year Worm castings are high
in bacteria, organic matter, and plant nutrients. Castings are 50 % organic
matter, with 11 trace minerals
• They leave numerous channels in the soil which may result in pesticides and
nutrients entering the subsoils at faster rates. These channels allow
preferential flow of water, rather than water moving only through the soil
pores.
They prefer a moist, non-acid environment. They also need organic
matter as food source, and high amount of available calcium.

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Arthropods (insects, crustaceans, arachnids, scorpions)

• are invertebrates (which can be microscopic or quire large)

• stir up and churn the soil, thereby aerating the soil
• they shred organic matter into small pieces, assisting other soil organisms in
the decomposition process
• they regulate populations of other soil organisms like protozoa, which help
maintain a healthy soil food web and control disease-causing organisms
• they are food of larger animals
• help distribute beneficial microbes in the soil
• help improve soil structure

Other macroorganisms – rodents, ground squirrel, arthropods, etc.

Classes of Microorganisms

a. Based on Carbon and Energy Source

Class Carbon Source Energy Source

Heterotrophs Organic Organic compounds

compounds
Autotrophs
Photoautotrophs CO2 Light
Chemoautorophs CO2 Inorganic
compounds

b. Based on Temperature Requirement

Psychrophiles - cold-loving-thrives below 20oC

Mesophiles - thrives best at temperature range of 25-35oC
Thermophiles - heat-loving-thrives at 45-65oC

c. Based on Oxygen Requirement

Aerobes or aerobic - must have access to O2

Anaerobes or anaerobic - grow only in the absence of O2
Facultative - develops either in the absence or presence of
O2
Kinds of Soil Microorganisms
a. bacteria
b. actinomycetes
c. fungi
d. algae
e. protozoa
f. nematodes

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Microorganisms may be subdivided into:

❖ pathogenic - invades and kills plants
❖ beneficial –often symbiotic with plant
❖ harmful – normally non-pathogenic opportunists on plants
❖ saprophytic – live on dead plants
❖ neutral – no specific effect on plants
Bacteria

❖ Single-celled
❖ many are heterotrophic
❖ many are aerobes, some anaerobic some are facultative aerobes (can
adopt to anaerobic condition),
❖ they multiply by binary fission or splitting of cells into two parts
❖ They form resting stages (spores) that survive dispersal by wind,
sediments, ocean currents and animal digestive tracts that has allowed
bacteria to spread to almost all soil environments.
❖ most diverse group of soil organisms; a gram of soil typically contains
20,000 different species. They have evolved mechanisms to adapt life
in the most extreme of environments, from the Antarctic to the
Amazon, from anaerobic wetlands to desiccated salt flats, from forest
litter to deep groundwater, from sodic soils at pH 10 to acid sulfate soils
at pH 2.
❖ important in bioremediation (because they can degrade pollutants)

As a group, they participate vigorously in virtually all of the organic transactions

that characterize a healthy soil system. Because soil bacteria as a group possess
such a broad range of enzymatic capabilities, scientists are now finding ways of
harnessing, even improving, the metabolic activities of bacteria to help with the
remediation of soils polluted by crude oil, pesticides, and various other organic
toxins. Bacteria are usually the most important group in the breakdown of
hydrocarbon compounds, such as gasoline and diesel fuel.

Classification by Shape
- rod-shape or bacilli – most abundant
- round-shaped or cocci
- spiral-shaped or spirilli – least common

Some Important Bacteria

N – fixing bacteria – Rhizobium, Azotobacter
Chemoautotrophic bacteria
N – Oxidizing bacter - Nitrosomonas - converts NH4+ to
NO2- Nitrobacter - converts NO2-
S – Oxidizing bacteria - TO NO3- Thiobacillus - converts S
to SO4+
Fe – Oxidizing bacteria - Thiobacillus ferrooxidans

Actinomycetes

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❖ Single-celled
❖ aerobic
❖ heterotrophic bacteria which are similar to fungi because they
form a branched filamentous network but less extensive than fungi.
The most abundant form of actinomycetes found in virgin and
cultivated soils belong to the genus Streptomyces. About 70-90
percent of actinomycete population in the soil are streptomycetes.
They have received considerable attention in research because of their
ability to synthesize toxic metabolites (ex. Aureomycin, terramycin,
neomycin). About ¾ of streptomycete isolates may produce anti-
microbial agents known as antibiotics. A popular example is
streptomycin. Actinomycetes are important in the decomposition of
relatively resistant residues such as chitin.

❖ They are much less competitive than bacteria and fungi in the
decomposition of fresh OM
❖ reproduce by spores
❖ particularly effective at breaking down tough substance like
cellulose and chitin (which make up the cell walls of fungi)
Fungi

❖ Aerobic
❖ Heterotrophic
❖ grow or germinate by spores
❖ form threadlike structure called mycelia which absorb nutrients.
❖ The fungi account for the largest part of the total microbial mass in
wellaerated soils.
❖ They are important in decomposing organic matter in acidic and
alkaline soils. As decomposers of organic matter, they are the most
versatile and persistent of any group. Cellulose, starch, gums and
lignin, as well as the more easily metabolized proteins and sugars,
succumb to their attack.
❖ Fungi play major roles in the process of humus formation and
aggregate stabilization. They carry out the largest share of the
decomposition in most cultivated soils.
❖ Fungi function more efficiently than bacteria in that they assimilate
into their tissues a larger proportion of the organic materials they
metabolize. Up to 50 % of the substances decomposed by fungi may
become fungal tissue, compared to about 20% for bacteria. Soil
fertility depends on on small degree on nutrient cycling by fungi, since
they continue to decompose complex organic materials after bacteria
and actinomycetes have ceased to function. Important groups of fungi
include Penicillium (source of penicillin) and Trichoderma which is
used in rapid composting. Trichoderma synthesizes large amounts of
cellulase, an enzyme which catalyze cellulose breakdown.

Algae

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Single-celled, others produce short filaments, photoautotrophs. They are

not important as decomposers of OM but are producers of new
photosynthetic growth.

Nematodes

❖ Nematodes are microscopic worms that feed on organic matter

and other soil animals, or infect root
❖ Under a hand lens (10X), nematodes appear transparent.
Parasitic nematodes are the most from an agricultural standpoint.
❖ Root-knot nematodes, Meloidogyne spp. are one of the
important parasitic nematode

Beneficial Effects of Soil Microorganisms

1. Organic matter decomposition –convert organically held nutrients to mineral

form. They also synthesize new compounds some of which help to stabilize soil
structure and contribute to humus formation.
2. Breakdown of toxic compounds
3. Transform unavailable elements to available forms
4. Nitrogen fixation and P solubilization
5. Plant protection

Distribution of Microorganisms in the Surface Soil

Table 9.1. Relative Numbers and Biomass of Fauna and Flora

Commonly Found in the Surface 15 cm of Soil
Organisms Number Biomass
Per m2 Per gram Kg/ha G/m2
Microflora
Bacteria 1013-1014 108-109 400-5000 40-500
Actinomycetes 1012-1013 107-108 400-5000 40-500
Fungi 1010-1011 105-106 1,000-15,000 100-1500
Algae 109-1010 104-105 10-500 1-50
Fauna
Protozoa 109-1010 104-105 20-200 2-20
Nematodes 106-107 10-10 2 10-150 1-15
Mites 103-106 1-10 5-150 .5-1.5
Collembola 103-106 1-10 5-150 .5-1.5
Earthworms 10-103 100-1500 10-150
Other fauna 102-104 10-100 1-10
Source: Brady, 1999. p 411

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Important association of Soil Microorganisms in Relation to

Higher Plants

Mycorrhiza - an association between fungus and higher plants wherein, the

fungus obtains carbohydrates and other growth components such as amino acids
and B vitamins from the plant while the plant, in turn, obtains its water and
nutrients through the fungus. Formation of mycorrhiza is markedly pronounced
in soils of low fertility particularly where N and P are limiting. Benefits from
mycorrhiza include:

1. Increased effective surface area of roots for absorption of water and

nutrients particularly P.
2. Increased drought and heat resistance.
3. Reduced infection by disease-causing organisms (protection from plant
pathogens).
4. Aid in Zn and Cu absorption

Two types of Mycorrhiza

Ectomycorrhiza - These fungi, stimulated by root exudates, cover the

surface of feeder roots with a fungal mantle. Their hyphae penetrate the
roots and develop on the free space around the cells of the cortex but do not
penetrate the cortex cell walls. On infertile soils, it is not uncommon for
ectomycorrhizal inoculation to increase growth by 50 to 500 percent

Endomycorrhiza- The most important members of endomycorrhiza

group are called arbuscular mycorrhizae (AM). Whem forming AM, fungal
hyphae actually penetrate the cortical root cell walls and, once inside the
plant cell, form small, highly branched structures known as arbuscules.
These structures serve to transfer mineral nutrients from the fungi to the
host plants and sugars from the plant to the fungus. Other structures called
vesicles, are usually also formed and serve as storage organs for the
mycorrhiza

Mycorrhizal Biofertilizers produced by BIOTECH-UPLB

1. Mycogroe – This is a soil-based fertilizer in tablet form which promotes
survival and growth of forestry species like eucalyptus, pines, agoho and
dipterocarps. The tablet is inoculated preferably during the nursery stage.
(P1.00/tablet in 1999)

2. Mykovam –Soil-based fertilizer which contains effective species of

mycorrhizal (VAM) fungi. It assists in the absorption of nutrients and water
from the soil and can be used for agricultural crops, fruit trees and forest
trees. The inoculant is added during the nursery phase at the rate of 3-4
grams (1 tsp) per plant. (P25.00 per kg).

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Biological Nitrogen Fixation

N – fixers make N2 available. Since they are photoautotrophic, they convert
CO2 to organic carbon. They colonize barren rocks, denuded and eroded
areas. N – fixing organisms are capable of fixing N because they synthesize
the enzyme nitrogenase that converts molecular nitrogen into ammonia.

Non-symbiotic N-fixers
Azotobacter
Clostridium
Beijerinckia
Some specialized BGA (blue-green algae or cyanobacteria)

Symbiotic N-fixers
Organism Genera Host Plant
Plant Group Location
Bacteria Rhizobium Legumes and inside
Bradyrhizobium parasponia nodules
Azorhizobium
Actinomycetes Frankia Betulaceae and Inside
8 family nodules
(trees)
Cyanobacteria Nostoc Bryophytes Leaf cavity
Nostoc Pteridophyte Leaf cavity
(Anabaena) (Azolla) – a
water fern
Nostoc Angiosperm Gland tissue

Azolla-anabaena complex - a symbiotic relation between the

nitrogenfixing blue-green algae, Anabaena azollae and an
aquatic fern under the genus Azolla. The algae live in cavities of
the fern’s upper lobes. When incorporated into the soil as green
manure, the fern decomposes and releases available N to the crop.
Rhizobium-legume symbiosis - Rhizobium bacteria live in the
nodules of the legumes where it conducts N fixation. The
Rhizobia derive their nutrients and energy from the legume. In
return, legumes derive their nitrogen from the rhizobia.

Major groups of rhizobia

Rhizobium-grow fast on culture media

Bradyrhizobium – grow slowly on culture media
Azorhizobium – grow slowly on culture media, capale f free-
living N fixation. Isolated from stem nodules of Sesbania rostrata

Associative N Fixation

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NFB are present around root, or inside plant tissues, and fix nitrogen, and
contribute to plant N nutrition.

Associative symbiosis - Bacteria enter the root and develop within the
cortical cells without forming nodules.

Examples: Paspalum notatum - Azotobacter paspali

Digitaria decumbens - Azospirillum lypoferum

BNF Biofertilizers produced by BIOTECH-UPLB

1. Nitro plus – A seed inoculant which contains an effective bacterium,

Rhizobium. It can substitute for inorganic nitrogen fertilizer of legumes
like peanut, mungbean, soybean, pole sitao, snap beans and cowpea.
(P20.00 per packet, for peanut- 4 packets per hectare).

2. Bio-N – Microbial-based fertilizer which contains the bacterium

Azospirillum specific for rice and corn. It enhances growth and
development of plants and provides 30-50% of their nitrogen
requirement. The inoculant is coated on the seeds of rice or corn before
they are sown. Rice seedlings may also be dipped in the inoculant
suspension before transplanting.

Bio-Organic Fertilizers developed by BIOTECH-UPLB

1. Bio-Green, Cocorich, etc.

Inoculated, enriched or processed compost that supplies nutrients to

plants, improves soil structure and nutrient availability and retards
moisture loss in the rhizosphere. It consists of agricultural and agro-
industrial wastes composted with suitable inocula (Trichoderma sp.)
and enriched with freeliving nitrogen-fixing bacteria (Azotobacter sp).
(Produced by the private sector and price averages at P175.00 per bag of
50 kg)

2. Bio-Quick – A fungus (Trichoderma sp) that can decompose organic

materials in 3-4 weeks (P20.00 per packet)

R. Bio-Fix – Azotobacter added to the compost heap for increased N content

of the final product. (P20.00 per packet)

Determining Abundance of Microorganisms in the Soil

a. direct microscopic examination
b. plate or viable count

Factors Affecting Microbial Population

Moisture, aeration, temperature, organic matter, pH, inorganic nutrient
supply. The optimum condition for microorganisms are: moisture content near

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field capacity, near neutral pH, high nutrient content, temperature near 30oC
(86oF).

Soil Organisms and Environmental Quality

Microorganisms are important in pesticide degradation. For example, in
the case of DDT, a synthetic pesticide against mosquitoes, the structure of DDT is
different from naturally occurring compounds and therefore few organisms have
enzymes that can degrade DDT.

Microbes detoxify pesticides in many ways such as, by shifting the chlorine
atoms, in some cases, the pesticides are degraded.

Hard pesticides – resist detoxification and/or degradation

Soft pesticides - easily degraded

Oil and natural gas decontamination – oil spill may displace soil air and
create an anaerobic soil.

SOIL ORGANIC MATTER

Important Contribution of Organic matter to soil properties

organic matter effects the physical, chemical and microbiological

properties of soils. One of the most distinct effects of organic matter is it’s makes
the color of the soil darker thereby generally indicating higher fertility level. As
an effective cementing agent, soil organic matter or humus also encourages soil
granulation with the concomitant benefit of increased aeration, permeability and
water holding capacity. Humus also reduces plasticity and stickiness which is
particularly important in heavy clays to make them more friable or easier to
cultivate.
Soil organic matter, by itself not only contributes nutrients, particularly N, P
and S but also the organic acids (for example, carbonic acid). Through carbonic
acids, nutrient elements are released from minerals. Organic matter, in colloidal
from has a very high cation exchange capacity that is nearly equal or even greater
than that of montmorillonite clay.
Organic matter serves as the source of carbon and energy of most soil
organisms. In addition, it is believed to contain growth-promoting substances
released during organic matter decomposition and which stimulates growth of
both plants and soil organisms.

Soil organic matter – a broad term for soil organic materials which includes
living and dead animals, plants, microorganisms, insects and other organic
materials.

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Sources of soil organic matter

Plants are the primary source of OM

In forest soils – leaves/leaf litter, roots, timber
In cultivated soils – crop residues
Animals are secondary source –animal wastes & animal remains

Composition of Green Plants

Water-75 %

Dry Matter –25%

Composition by Organic compounds Composition by elements

Cellulose – 45% by weight Carbon-42%

Hemicellulose – 18% Oxygen – 42%
Lignin –20% Hydrogen- 8%
Protein-8% Ash- 8%
Sugars and starches – 5%
Fats and waxes- 2%
Polyphenols –2%

Rate of decomposition
1. Sugars, starches, and simple proteins rapid decomposition
2. Crude proteins
1. Hemicelluloses
2. Cellulose
3. Fats. Waxes, etc.
4. lignins and phenolic compounds very slow
decomposition

Decomposition of organic compounds in aerobic

soils Three separate simultaneous processes can be
distinguished:

1. carbon compounds are enzymatically oxidized to produce carbon

dioxide, water, energy, and decomposer biomass;
2. The essential nutrient elements such as N, P, and S are released and/or
immobilized by a series of specific reactions that are relatively unique for
each element;

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3. Compounds very resistant to microbial action are formed, either

through modification of compounds in the original tissue or by microbial
synthesis.

Decomposition Products

Aerobic decomposition

Carbon – CO2. HCO3, CO3

Nitrogen – NH4, no3
Sulfur – SO4
Phosphorus – H2PO4, HPO4
Others – H2O, H, K, Ca, Mg, Na

Anaerobic decomposition (where there is insufficient O2)

CO2, CH4, reduced S compounds, Hydrogen,

volatile fatty acids – acetic acid, propionic acid, isobutyric acid

Factors Affecting decomposition

Plant growth stage- young plants are easily decomposed because they have
more of the easily decomposable organic compounds; old plants have
more woody tissues made up mainly of lignin which is very resistant
to decomposition
C:N ratio- with narrow C:N ratio, there is relatively higher amount of N,
hence faster decomposition rate

➢ C content of typical plant dry matter is 42 %

➢ C content of SOM ranges from 40-50 %
➢ N content of plant residues is much lower and varies
widely from <1 to >6%

Microbes must incorporate 8 parts carbon to every one-part nitrogen (8

:1)
Critical C:N ratio – 25:1

C:N ratio of some selected organic residues

Humus 10:1
Farmyard manure 20:1
Young beans 22:1
Mature beans 53:1
Rice (young) 25:1
Rice (mature) 75:1
Sugarcane trash 50:1
Sawdust 400:1

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Lignin and polyphenol content- polyphenol compounds form complexes

with proteins during residue decomposition hence slow the rates of N
mineralization and C oxidation.
Oxygen –needed by aerobes
Moisture
Temperature
Soil pH
Soil texture

Direct influence of humus on plant growth

• Production of organic compounds which are absorbed by plants:
e.g soluble organic N and organic P
• Growth promoting compounds such as vitamins, amino acids,
auxins, gibberellins
• Small quantities of fulvic and humic acids in soil solution which
enhance certain aspects of growth
• Allellochemical effects – allellopathy is a process by which one
plant infuses the soil with a chemical that affects the growth of higher
plants, either by exuding allellochemicals or the compounds may be
leached out of the plant foliage by through-fall in rainwater. In other
cases, thru microbial metabolism of plant tissues.

Indirect influences of organic matter on plant growth

• Provides much of the cation exchange & water-holding capacity of most
surface soils
• Certain components are responsible for stabilization of aggregates
• Contains large quantities of plant nutrients especially nitrogen
• Supplies energy and body-building constituents for most
microorganisms

Composts and Composting

Composting is the practice of creating humuslike organic materials outside of
the soil by mixing, piling or otherwise storing organic materials under
conditions conducive to aerobic decomposition and nutrient conservation.
The decomposition processes and organisms involved are the same as in
natural humus formation except that decay occurs outside of the soil, and in
such a concentrated fashion as to generate considerable heat.

Three Stages in composting

1. A brief initial mesophilic stage where sugars and readily available
microbial food sources are rapidly metabolized, causing the temporature in
the compost pile to gradually rise from ambient to 40oC.
2. A thermophilic stage occurs during the next week or two, during which
temperatures rise to 50 to 75oC while thermophilic organisms decompose
cellulose and other more resistant materials. Frequent mixing during this
state is essential to maintain oxygen supply and assure even heating of all
the materials.. The easily decomposed compounds are used up, and
humuslike compounds are formed during this stage.

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3. A second mesophilic or curing stage follows, during which temperature

falls back to near ambient, and the material is recolonized by mesophilic
organisms, including certain beneficial organisms.

Transformation of N
Nitrogen fixation –reduction of atmospheric nitrogen gas (N2) to
ammonia (NH3)
Biological Nitrogen fixation – can only be done by a specialized group of
microorganisms in the presence of nitrogenase enzyme which catalyzes
the reduction of dinitrogen gas (in the atmosphere) to ammonia.

N2 + 6 e- + 8 H 2NH3 + H2

Nitrogenase + Fe & Mo

The ammonia is now combined with organic acids to form amino acids
and proteins.

Non Biological N fixation

In the atmosphere, molecular N is modified through lightning. The energy
released by electrical discharges breaks the strong bonds between nitrogen
atoms, causing them to react with oxygen. In this process, N is oxidized and
oxygen is reduced.

Lightning + N2 + O2 2 NO (nitrous oxide)

Industrial N Fixation (Haber-Bosch process)

• Ammonification (Mineralization of organic-N). Microbial

decomposition of plant and animal residues in soil releases mineral
nitrogen, nitrate and ammonium, forms of N that plants can absorb from
the soil solution. Soil organic matter is also constantly slowly decomposing
(even as new soil organic matter is being formed), releasing a slow trickle of
nitrate and ammonium into the soil solution. In the soil, NH3 is rapidly
converted to NH4+ when H+ are plentiful.

Forms of organic N in the soil

Humic substances (ring compounds) –50 %

Amino acids – 25-40 %

Amino sugars – 5-10 %

purines & pyrimidines - > 5%

• Immobilization –utilization of mineral N by microorganisms, hence N become

tied up on the cells as organic N

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Ammonium fixation (a form of immobilization)

By clays (ammonium becomes trapped in clay layers: cations Ca, Mg and Na

expand the lattice while K contract the lattice)

▪ illite
▪ Vermiculite
▪ Montmorillonite

• Ammonia volatilization - Under high pH, NH4+ becomes ammonia hence,

volatilization increases.

NH4+ + H2O + OH- NH3 + 2H2O

• Nitrification – conversion of NH4+ to NO3- . This aerobic reaction is carried

out by autotrophic bacteria (Nitrosomonas and Nitrobacter). Maximum
nitrification occurs at neutral pH and at high temperatures (favorable to the
bacteria).
nitrosomonas
2 NH4+ + 3O2 2NO2- + H2O + 4H+ +
energy
(1)

nitrobacter
2NO2- + O2- 2NO3- + energy
(2)

In upland soils, ammonium undergoes nitrification, hence the dominant

form of N in upland soils is nitrate. In flooded soils, ammonium
accumulates because nitrification requires oxygen.

• Denitrification – biochemical reduction of NO3-N to N2 under low oxygen

levels (anaerobic condition). Organisms use the oxygen in the nitrate as terminal
electron acceptor. Example, Pseudomonas use NO 3- instead of O2 as terminal
electron acceptor. Denitrification is accelerated under flooded or compacted
condition and high N inputs.

-2(O) -2(O) - (O) - (O)

2HNO3 2HNO2 N2O N2
2NO
nitrate nitrite nitrous oxide elemental N nitric
oxide

• Leaching - loss of nitrate through moving water

➢ greater in coarse-textured soils and under high rainfall

➢ leaching is reduced if there is vegetation leached nitrate N may pollute
water resources

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D. Activities/Exercises

Directions: Please do this activity to a separate paper.

Critic Paper. Research one published journal article about Biological Nitrogen Fixation with the publication year
of 2015 up to 2020). Start to analyze the article as how the researchers conduct the experiment, interpret the result
and discuss the impact of the results.
Help tips!
Following these steps can help you make better sense of the material as you assess what you are reading.

1. Read the introduction section of the article. Is the hypothesis clearly stated? Is necessary background
information and previous research described in the introduction? In addition to answering these basic questions,
you should take note of information provided in the introduction and any questions that you may have.

2. Read the methods section of the article. Is the study procedure clearly outlined in the methods section? Can
you determine which variables the researchers are measuring? Remember to jot down questions and thoughts that
come to mind as you are reading. Once you have finished reading the paper, you can then refer back to your initial
questions and see which once remain unanswered.

3. Read the results section of the article. Are all tables and graphs clearly labeled? Do researchers provide enough
statistical information? Did the researchers collect all of the data needed to measure the variables in question?
Again, make note of any questions you have or any information that does not seem to make sense. How do the
researchers interpret the results of the study? Did the results support their hypothesis? Do the conclusions drawn
by the researchers seem reasonable? The discussion section offers students a good opportunity to take a position.
If you agree with the researcher's conclusions, explain why. If you feel that the researchers are incorrect or off-
base, point out problems with the conclusions and suggest alternative explanations. Another alternative is to point
out questions that the researchers failed to answer in the discussion section.

Begin Writing Your Own Critique of the Paper

Once you have read the article, compile your notes and develop an outline that you can follow as you write your critique
paper. Use the following guide to help structure your critique paper:

1. Introduction. Begin your paper by describing the journal article and authors you are critiquing. Provide the main
hypothesis or thesis of the paper and explain why you think the information is relevant. statement. Your thesis
statement is the main idea of your critique. Your thesis should briefly sum up the main points of your critique.

3. Article Summary. Provide a brief summary of the article, outlining the main points, results and discussion. Be
careful not to get too bogged down by your summary. Remember, this section of your paper should highlight the
main points of the article you are critiquing. Don't feel obligated to summarize each little detail of the main paper.
Focus instead on giving the reader an overall idea of the content of the article.

3. Your Analysis. Describe any problems you had with the authors premise, methods, or conclusions. Your
critique might focus on problems with the authors argument, presentation or on information, and alternatives that
have been overlooked. Organize your paper carefully and be careful not to jump around from one argument to the
next. Argue one point at a time. Doing this will ensure that your paper flow's well and is easy to read.

4. Conclusion. Your critique paper should end with an overview of the articles argument, your conclusions and
your reactions.

Format: Georgia, 12 font size, Black font color, Short bond paper, Justify

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E. Post-test/Evaluation.

Directions: Read carefully and answer the following questions. Answer on

separate sheet of paper. This is a graded exam. This test will evaluate how much
your effort to learn this topic.

Test 1. Multiple Choice. Choose the letter of the correct answer.

1. The most numerous and most diverse group of soil microorganisms are?
a. fungi b. bacteria c. algae d. actinomycete
2. Among the soil animals, the most diverse group are the?
a. Annelids b. Helminths c. Arthropods d. worms
3. Nitrogen is the most limiting element in crop production, except for legumes.
The available form of nitrogen is?
a. Organic matter b. Ammonium c. Nitrate d. Both b and c
4. Association between plant root and fungi is known as?
a. Lichen b. Competition c. Symbiosis d. Mycorrhiza
5. Of the following, the one that is not carbohydrate is?
a. Lignin b. Cellulose c. Starch d. Hemicellulose

II. Modified true or False. Write true on your answer sheet if the
statement is true, if false, write the word that makes the statement
wrong.
1. Fungi being heterotrophic organisms use organic carbon as their energy source
(T/F)?
2. Denitrification results in the loss of N in the form of either N2 or N2O (T/F)? 3.
Nitrification occurs under anaerobic condition while denitrification occurs under
aerobic condition (T/F)?
4. As the organic material decomposes, the C and N contents also decrease and
the C:N ratio becomes narrow (T/F)?
5. Plant materials with wide C:N ratios are slowly decomposed while those with
narrow C:N ratios are easily decomposed (T/F)?
6. Legumes have narrow C:N ratios and are therefore easy to decompose (T/F)?
7. Mineralization of N occurs in a decomposing organic material when its C:N ratio
is greater than 20:1 (T/F)?
8. When there is net mineralization or when there is more mineralization than
immobilization, N is said to be available (T/F)?
9. OM can improve soil texture (T/F)?
10. Composting is the practice of creating humus-like organic materials outside of
the soil by mixing, piling or otherwise storing organic materials under
conditions conducive to aerobic decomposition and nutrient conservation
(T/F)?

III. Discussion. Write your answer on your answer sheet.

1. Explain the processes and the microorganisms involved in biological

nitrogen fixation.

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2. How the C:N ratio affects the rate of decomposition of organic matter.
Elaborate your answer.

References

Book

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Paul, E. A. (2015). Soil Microbiology, Ecology and Biochemistry. (4th edition).

Journal

Aislabie, J., & Deslippe, J.R. (2013). Soil microbes and their contribution to soil
services. In Dymond JR ed. Ecosystem services in New Zealand – conditions and
trends.Manaaki Whenua Press, Lincoln, New Zealand.

Bready, N.C. (1989). Nature and properties of soils. New York: MacMillan Publishing
Co. Inc.

Coskan, A., & Dogan, K. (2011). Symbiotic Nitrogen Fixation in Soybean. Soybean
Physiology and Biochemistry. Süleyman Demirel University, Mustafa Kemal
University. Turkey.

Frate, C. (2007). “Nitrogen Transformations in Soil”. University of California

Cooperative Extension, Tulare County.

Habte, M. (2000). Mycorrhizal Fungi and Plant Nutrition. Plant Nutrient

Management in Hawaii’s Soils, Approaches for Tropical and Subtropical Agriculture
J. A. Silva and R. Uchida, eds. College of Tropical Agriculture and Human Resources,
University of Hawaii at Manoa, ©2000.

Herschkovitz, Y., Lerner, A., Davidov, Y., Rothballer, M., Hartmann, A., &

Jurkevitch, E. (2005). Inoculation with the Plant-Growth-Promoting hizobacterium

Azospirillum brasilense Causes Little Disturbance in the Rhizosphere and Rhizoplane
of Maize (Zea mays). Department of Plant

Pathology and Microbiology, Faculty of Agricultural, Food and

Environmental Quality Sciences, The Hebrew University of Jerusalem, P.O. Box 12(
Rehovot 76100, Israel. Received: 13 July 2004 / Accepted: 4 November 2004 / Online
publication: 13 October 2005.

Martin, A. (1977). Introduction to soil microbiology. Second edition. Cornell

University.copyright 1977. New York.p 1-103.

Misra, R.V., Roy, R.N., & Hiraoka, H. (2003). On farm composting methods. FAO.

Silva, J. A., & Uchida, R. (2000). Plant nutrient management in Hawaii’s soils,
approaches for tropical and subtropical agriculture. College of Tropical Agriculture
andHumanResources, University of Hawaii at Manoa, ©2000. 3728BBS.Introduction
to environmental microbiology and (Microbial ecology).

Willey, J.M., Sherwood, L.M., & Woolverton, C.J. (2008). Microbiology. McGrawHill
Co. Inc. New York.

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