SLM 505 Soil Microbiology and Biochemistry

COURSE
GUIDE
SLM 505
SOIL MICROBIOLOGY AND BIOCHEMISTRY
Course Team Dr. Nkechi N.M. Chinke(Course Writer) -

Ahmadu Bello University, Zaria
Dr. Sabo Elizabeth (Programme Leader) -
NOUN
Mr. Awolumate Samuel (Course
Coordinator) - NOUN
Dr. Aliyu Musa (Course Editor) - NOUN
NATIONAL OPEN UNIVERSITY OF NIGERIA

SLM 505 COURSE GUIDE
© 2023 by NOUN Press

National Open University of Nigeria
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e-mail: [email protected]
URL: www.nou.edu.ng
All rights reserved. No part of this book may be reproduced, in any

form or by any means, without permission in writing from the publisher.
Printed 2017, 2023
ISBN: 978-058-044-X
ii
CONTENTS PAGE
Introduction………………………………………………….. iv
What you will learn in this course…………………………… iv
Course Aims………………………………………………… iv
Course Objectives…………………………………………… v
Working through this Course……………………………….. vi
Course Materials…………………………………………….. vi
Study Units………………………………………………….. vi
References and Further Reading…………………………….. vii
Assignment File……………………………………………… ix
Assessment………………………………………………….. ix
Tutor Marked Assignment…………………………………… ix
Final Examination and Grading……………………………… ix
Presentation Schedule………………………………………... x
Course Marking Scheme…………………………………….. x
Course Overview…………………………………………….. x
How to get the Most from this Course………………….......... xii
Facilitators/Tutors and Tutorials……………………………... xii
Summary……………………………………………………... xiii
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INTRODUCTION
SLM 505 a two credit course is a comprehensive course for the study of
soil microbiology and biochemistry, designed for use by advanced
undergraduate students who wish to have an overview of the subject to
those who need to have a comprehensive knowledge of the field of soil
microbiology and biochemistry.
The course has 25 units divided into five broad subject areas, starting
with background and continuing through the soil biota, interactions
between organisms, microbial transformations, biochemistry (enzymatic
activities) and concluding with the impact of human processes through
pesticide applications. These topics therefore will attempt to improve the
understanding required to provide a foundation for the inter-disciplinary
approaches that will continue to provide exciting new ideas in the field
of agriculture.
You are encouraged to devote, at least two hours studying each of the 25
units. You are also advised to attempt the self-assessment exercises as
they are important for better understanding of the units. You are advised
also to pay attention to the Tutor – Marked Assignments (TMA) (details
provided in a separate file).
There will be tutorial classes. Details of location of the tutorials and time
will be made known to you; this is a great opportunity for you to have
direct contact with your course coordinator. Areas not understood in the
course of study will be properly explained.
WHAT YOU WILL LEARN IN THIS COURSE
The overall aim of this course is for you to have a comprehensive

knowledge of the field of soil microbiology and biochemistry. An
understanding of this course is important to further understanding
agricultural and environmental impacts on life. During the course
therefore, you will learn about the importance of microorganisms in the
soil environment and you will be furnished with knowledge to solve
issues related to the functions of other biological systems on earth –
biochemistry (the chief support or engine room of soil microbial
functioning).
COURSE AIMS
The aim of the course is to give you a better and comprehensive

understanding of the microorganisms living in the soil and their
activities that are of agricultural and environmental significance. The
aim of the course will be achieved by:
iv
• Introducing you to the origin and contributions of soil

microbiology to agriculture.
• Introducing you to the organisms in the soil.
• Helping you to understand the importance of soil organisms.
• Giving an insight into the microbiology of the rhizosphere.
• Exposing you to the interrelationships of organisms in the soil.
• Helping you to understand transformations mediated by
microorganisms.
• Helping you to understand biochemical functioning in the soil
environment.
• Introducing you to application of pesticides and their importance
in agricultural ecosystems.
• Helping you to understand the effects of pesticides on soil
microflora.
COURSE OBJECTIVES
To achieve the aims mentioned above, the course sets overall objectives.
In addition, each unit has its specific objectives. The unit objectives are
given at the beginning of the unit; you should read them before you start
working through the unit. You may also want to refer to them during
your study of the unit so as to check on your progress. You should
always look at the unit objectives after completing a unit. By this, you
can be sure that you have done what was required of you by the unit.
Below are the broader objectives of the course, as a whole. By meeting

these objectives, you should have achieved the aims of the course as a
whole. On completion of the course, you should successfully be able to:
• define soil microbiology and soil biochemistry
• explain the importance of soil microbiology and biochemistry in
terms of their contributions to agriculture
• explain the major types of soil organisms in the soil habitat and
their beneficial roles in agriculture
• explain the factors affecting soil organisms
• explain microbiology of the rhizosphere concepts
• discuss the effect of plants on microorganisms
• describe the types of microbial soil interactions
• explain transformations mediated by microorganisms such as
organic matter, nitrogen, phosphorus, sulphur and iron
• define and classify enzymes
• state the enzymes important in agricultural ecosystem and why?
• discuss the functions of enzymes
• discuss the factors affecting enzyme activities
• define basic concepts in enzyme reactions
v
• explain enzyme kinetics and the transformations of Michaelis-

Menten equation
• explain enzyme inhibition and various types of inhibition
• define pesticide and state the types of pesticides
• explain the merits and demerits of pesticides
• discuss microbial degradations of pesticides
• discuss the effects of pesticides on soil microorganisms.
WORKING THROUGH THIS COURSE
To complete this course you are required to read the study units, as well
as other related materials. Each unit contains self-assessment exercises,
and at certain points in the course, you are required to submit
assignments for assessment purposes. At the end of the course, you are
going to sit for a final examination. The course should take you about
18/ 21 weeks in total to complete. Below you will find listed all the
components of the course, what you have to do and how you should
allocate your time to studying the course.
COURSE MATERIAL
The first five units center on the fundamentals and brief history of soil
microbiology and biochemistry and the organisms that live in the soil;
Module 1.The next five units that address the microbiology of the
rhizosphere and the interactions among microorganism and between
microorganisms and plants;Module 2has units 11 – 15 highlights the
microbial transformation of cycles in soil and factors affecting them –
Module 3 andModule 4 comprising of units 16 – 18 deals with enzymes
and their reactions in soil; while Module 5having units 19 – 22 deals
with the effect of pesticides, especially on soil microorganisms.
The major components of the course include the following:

1. Course Guide
2. Study Units
3. Textbooks and References
4. Assignment File
5. Presentation Schedule
STUDY UNITS
There are 25 study units in this course as follows:
Module 1 Fundamentals
Unit 1 Introduction and Brief History of Soil Microbiology
vi
Unit 2 Introduction to Soil Biochemistry

Unit 3 TheSoil Habitat
Unit 4 Microbial Composition of Soil (Soil Organisms)
Unit 5 Physiology of Microbial Growth
Module 2 Microbiology of the Rhizosphere and Microbial

Interactions
Unit 1 RhizosphereSoil
Unit 2 Soil Microbial Interactions
Unit 3 Non-Symbiotic VsSymbiotic Associations
Unit 4 Rhizobium Association
Unit 5 MycorrhizalAssociation
Module 3 Microbial Transformations of Cycles in Soil
Unit 1 Soil Organic Matter Transformation

Unit 2 Nitrogen Transformation
Unit 3 Phosphorus Transformation
Unit 4 SulphurTransformation
Unit 5 Micronutrient Iron (Fe) Transformation
Module 4 Soil Enzymes
Unit 1 What are Enzymes?

Unit 2 Enzymes Classification and Nomenclature
Unit 3 Soil Enzymes Importance in Agriculture
Unit 4 Kinetics of Enzyme Reactions in Soil
Unit 5 Enzyme Inhibition
Module 5 Pesticides in Soil
Unit 1 Nature of Pesticides

Unit 2 Behavior of Pesticides in Soil
Unit 3 Effect of Pesticides on Soil Organism
Unit 4 Biodegradation of Pesticides
Unit 5 Pesticide Persistence in Soil
Text Books and References
Experience in teaching this subject has shown that you often stumble
over many new terms that are introduced during the course of study. To
help you overcome this obstacle, a comprehensive description or
explanation of soil microbiology terms is given under each unit or where
appropriate.
vii
You should note that bolded terms in each unit are defined in the text.
Recommended textbooks and references are listed below:
1) Alexander, M. (1991). Introduction to Soil Microbiology.
(2nded.). Wiley, New York.
2) Alexander, M. (1994). Biodegradation and Bioremediation.
Wiley, New York.
3) Atlas, R.M. &Bartha, R. (1981). Microbial Ecology:
Fundamentals and Applications.Reading,
Massachusetts:Addison-Wesley Publishing Company.
4) Bala, A. (2012). Lead Farmer Training.In:Biological Nitrogen
Fixation and Grain Legume Enterprise.Adapted by
AbdullahiBala for the Training ofTrainers and Lead Famers
within theN2Africa West Africa Outreach Project..
5) Brady, N.C.&Weil, R.R. (2002). The Nature and Properties of
Soils.(13thed.).Prentice Hall, Upper Saddle River.
6) Eldor, A.P. (Ed.). (2007). Soil Microbiology, Ecology and
Biochemistry. (3rded.). Canada:Academic Press Publications..
7) Hassan, G.D. (2010). Soil Microbiology and Biochemistry. New
India Publishing Agency.
8) Lynch, J.M. &Hobbie, J..E. (1988). Microorganisms inAction:
Concepts andApplication.In:Microbial Ecology. Blackwell,
Oxford.
9) Maier, R. M; Pepper, I. L&Gerba, C. P. (2009). Environmental
Microbiology.San Diego, California:Academic Press.. 589pp.
10) Nannipieri, P., Kandeler, E. &Ruggiero, P. (2002). Enzyme
Activities and Microbiological and Biochemical Processes in
Soil. In: R.S. Burns andR.P. Dick (Eds.). “Enzymes inThe
Environment Activity, Ecology And Applications. New
York:Dekkers.
11) Nelson, D.L. &Cox, M.M. (2002). Lehninger Principles of
Biochemistry. (3rded.). New York: New Delhi Worth Publishers.
12) Palmer, T. (2001). Enzymes: Biochemistry, Biotechnology and
Chemical Chemistry. (3rded.). England: Horwood Publishing,
Chichester.
13) Price, N.C. &Stevens, L. (1999). Fundamentals ofEmzymology.
(3rded.). Oxford:Oxford University Press.
14) Soil Science Society ofAmerica (1997). Glossary of Soil Science
Terms. SSSA, Madison, WI. 138pp. Available Online At
Www.Soils.Org/Sssagloss/.
15) Sylvia, D.M., Hartel, P.G., Fuhrmann, J.J. &Zuberer, D.A.
(2005). Principles and Applications of Soil Microbiology.
(2nded.).New Jersey: Prentice Hall, Upper Saddle River.
16) Wilson, K. &Walker, J. (Eds.). (2000). Principles and
Techniques of Practical Biochemistry. (5thed.). Cambridge
University Press.
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ASSIGNMENT FILE
In this file, you will find the details of the work you must submit to your
tutor for marking. The marks you obtain will form part of your total
score for this course.
ASSESSMENT
There are two aspects to the assessment of this course. The first being
the Tutor-Marked Assignments (TMA) and the second the final written
examination. You are advised to attempt the exercises as this will help
you apply the information, knowledge and techniques learnt during the
course.
The assignments must be submitted to your tutor for formal assessment

in accordance with the deadlines stated in the presentation schedule and
assignment file. The work you submit to your tutor for assessment will
count for 30% of your total course mark. At the end of the course, you
will sit for a final examination; this examination will count for 70% of
your total course mark.
TUTOR – MARKED ASSIGNMENT
You are advised to submit your assignments as required. Each

assignment counts for 6% of your marks for the course. You should be
able to complete your assignment from the information obtained from
the study units and other recommended texts. However, it is advisable
that you research more and study other references as this will give you a
broader view point and many provide a deeper understanding of the
subject.
When you complete each assignment, send it to your tutor. Make sure
that each assignment reaches your tutor on or before the deadline given
in the presentation schedule and assignment file. If for any reason, you
cannot complete your work on time, contact your tutor to discuss the
possibility of an extension. Extensions will not be granted after the due
date, except for exceptional circumstances.
FINAL EXAMINATION AND GRADING
The final examination for this course will take three hours and have a
value of 70% of the total course grade. The examination will consist of
questions which reflect the types of self-assessment exercises and tutor-
marked assignments you have previously encountered. All areas of the
course will be assessed. Take time to revise the entire course before the
examination. The examination covers all parts of the study units.
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PRESENTATION SCHEDULE
Your course materials will give you important dates for attending
tutorials and the timely completion and submission of your tutor-marked
assignments. Remember that you are required to submit all assignments
by the due date. Please guard against lagging behind in your work.
COURSE MARKING SCHEME
The following table shows how the marking scheme is divided.
Table 1: Course Marking Scheme
Assignment Marks
Assignments 1 – 5 Five assignments count for 6%
each = 30% of course marks
Final examination 70% of overall course marks
Total 100% of course marks
COURSE OVERVIEW
This table brings together the units, the number of weeks you should
take to complete them and the assignment that follows.
Table 2: Course schedule
Units Title of Work Weeks Assessment (end

activity of each module)
Course Guide
Module 1: Fundamentals
1 Introduction and Brief History of 1 Assignment 1
Soil Microbiology
2 Introduction to Soil Biochemistry 1
3 The Soil Habitat 1
4 Microbial Composition of Soil 1
(Soil Organisms)
5 Physiology of Microbial Growth 1
Units Title of Work Weeks Assessment

Module 2: Microbiology of the activity (end of each
Rhizosphereand Microbial module)
Interactions
1 RhizosphereSoil
2 Soil Microbial Interactions 1
3 Non-Symbiotic VsSymbiotic 1 Assignment 2
x
Associations
4 Rhizobium Association 1
5 MycorrhizalAssociation 1
Units Title of Work Weeks Assessment

Module 3: Microbial activity (end of each
Transformations of Cycles in Soil module)
1 Soil Organic Matter Transformation 1
2 Nitrogen Transformation 1
3 Phosphorus Transformation 1 Assignment 3
4 SulphurTransformation 1
5 Micronutrient Iron (Fe) 1
Transformation

Module 4: Soil Enzymes activity of each module)
1 What are Enzymes? 1
2 Enzymes Classification and 1
Nomenclature Assignment 4
3 Soil Enzymes Importance in 1
Agriculture
4 Kinetics of Enzyme Reactions in 1
Soil
5 Enzyme Inhibition 1

Module 5: Pesticides in Soil activity of each module)
1 Nature of Pesticides 1
2 Behavior of Pesticides in Soil 1
3 Effect of Pesticides on Soil 1 Assignment 5
Organism
4 Biodegradation of Pesticides 1
5 Pesticide Persistence in Soil 1
Revision 1
Examination 25
xi
HOW TO GET THE MOST FROM THIS COURSE?
In distance learning, the study units replace the conventional university

lecturer. This is one of the advantages of distance learning; you can read
and work through specially planned study materials at your own pace,
time and place that suits you best.
Each of the study units follows a common format. The first item is an
introduction to the subject matter of the unit and how a particular unit is
integrated with other units. Next is a set of learning objectives. These
objectives let you know what you should be able to do by the time you
have completed the unit. You should use these objectives to guide your
study. When you have finished the unit, you must go back and check
whether you have achieved the objectives. If you make this a habit you
will improve significantly your chances of passing the course.
FACILITATORS/TUTORS AND TUTORIALS
There are 20 hours of tutorials provided in support of this course. As

soon as you are allocated a tutorial group, you will be notified of the
dates, times and location of tutorials, together with the name and phone
number of your tutor.
Your tutor will mark and comment on your assignments; he/she will
keep a close watch on your progress and on any difficulties you may
encounter and provide assistance to you during the course. You must
mail your tutor-marked assignments to your tutor well before the date
due (at least two working days are required). They will be marked by
your tutor and returned to you as soon as possible.
Do not hesitate to contact your tutor by telephone, e-mail or via the

discussion board if you need help. The following might be
circumstances in which you would find help necessary. Contact your
tutor if:
• You do not understand any part of the study unit
• You have difficulty with the assignments/exercises
• You have a question or problem with your tutor’s comments on
any assignment or with the grading of an assignment
Try your best to attend tutorials as this is the only chance to have face to
face contact with your tutor and to ask questions. You can ask questions
on any problem encountered during the course of your study. To gain
maximum benefit from the tutorials, make a list of questions before
hand and participate actively in the discussions.
xii
SUMMARY
Soil microorganisms and the biochemical reactions they carryout in the

soil play major role in nutrient release and nutrient use efficiency. When
you consider the health of the soil or the quality of the soil using
biochemical compounds released that enhance or improve microbial and
biochemical activities in soil, the importance of soil microbiology and
biochemistry will be understood by you and productivity of soils will be
improved leading to enhanced crop yield on a sustainable basis which is
the ultimate goal of the small scale farmer. The important questions that
require answer shows that many of the new ideas in agriculture will
come through the study of the physiology and ecology of soil organisms,
including processes they carry out such as nutrient transformations and
biogeochemical cycles.
This course (SLM 505), therefore has topics on the physiology to

biochemistry of soil organisms as well as on ecology in an attempt to
improve the understanding needed to have a foundation for the
interdisciplinary approaches that will continue to provide exciting new
concepts in the field of agriculture.
We wish you the best and hope that you will find the course both
interesting and useful. All the best.
xiii
MAIN
COURSE
CONTENTS PAGE
Module 1 Fundamentals…………………………... 1
Unit 1 Introduction and Brief History of Soil
Microbiology …………………………….. 1
Unit 2 Introduction to Soil Biochemistry………. 6
Unit 3 TheSoil Habitat…………………………... 9
Unit 4 Microbial Composition of Soil
(Soil Organisms)…………………………. 12
Unit 5 Physiology of Microbial Growth………... 17
Module 2 Microbiology of the Rhizosphere
and Microbial Interactions…………….. 20
Unit 1 RhizosphereSoil………………………… 20
Unit 2 Soil Microbial Interactions ………………. 28
Unit 3 Non-Symbiotic Vs Symbiotic Associations 33
Unit 4 Rhizobium Association…………………… 41
Unit 5 MycorrhizalAssociation………………….. 44
Module 3 Microbial Transformations of Cycles
in Soil…………………………………… 51
Unit 1 Soil Organic Matter Transformation…….. 51
Unit 2 Nitrogen Transformation………………… 56
Unit 3 Phosphorus Transformation……………... 61
Unit 4 SulphurTransformation………………….. 65
Unit 5 Micronutrient Iron (Fe) Transformation… 69
Module 4 Soil Enzymes……………………………. 72
Unit 1 What are Enzymes? ……………………... 72
Unit 2 Enzymes Classification and Nomenclature. 78
Unit 3 Soil Enzymes Importance in Agriculture..... 86
Unit 4 Kinetics of Enzyme Reactions in Soil…...... 91
Unit 5 Enzyme Inhibition………………………… 100
Module 5 Pesticides in Soil………………………..... 106
Unit 1 Nature of Pesticides ……………………..... 106
Unit 2 Behavior of Pesticides in Soil…………….. 113
Unit 3 Effect of Pesticides on Soil Organism…..... 118
Unit 4 Biodegradation of Pesticides……………… 121
Unit 5 Pesticide Persistence in Soil………………. 124
SLM 505 MODULE 1
MODULE 1 FUNDAMENTALS
Unit 1 Introduction and Brief History of Soil Microbiology

Unit 2 Introduction to Soil Biochemistry
Unit 3 TheSoil Habitat
Unit 4 Microbial Composition of Soil (Soil Organisms)
Unit 5 Physiology of Microbial Growth
UNIT 1 INTRODUCTION AND BRIEF HISTORY OF

SOIL MICROBIOLOGY
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Brief History of the Origin of Soil Microbiology
3.2 Some Important Names in Soil Microbiology
3.3 What is Soil Microbiology
3.4 Importance of Soil Microbiology in Agriculture
4.0 Conclusion
5.0 Summary
6.0 Tutor-Marked Assignment
7.0 References/Further Reading
1.0 INTRODUCTION
Soil microbiology may be broadly defined as the study of

microorganisms and their processes in soil. The interaction of
organisms in the soil with each other and their environment is called soil
ecology while soil biochemistry involves microbial processes, soil
enzyme activities, formation and turnover of soil organic matter.
In this unit you will be looking at the origin of soil microbiology and the
contributions of some of the early founders of soil microbiology. Also
the importance of soil microbiology in agricultural ecosystems will be
studied.
2.0 OBJECTIVES
At the end of this unit, you should be able to:
• define soil microbiology

• state some important names in soil microbiology and their
contributions
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SLM 505 SOIL MICROBIOLOGY AND BIOCHEMISTRY
• discuss the importance of soil microbiology in agriculture.
3.0 MAIN CONTENT
3.1 Brief History of the Origin of Soil Microbiology
The origin of soil microbiology is linked with the development of

microbiology as a science and cannot be understood alone. The first
documented fact of soil and soil biota, originates in the East by the
Chinese. They classified soils and regarded earthworms as “angels of the
earth” while the Romans saw earthworms as “intestines of the earth”.
They classified soil based on colour (organic matter content) and saw
the importance of land forms, erosion, vegetation, land use and human
health implications. Fungi were the 1st microorganisms to be classified
because of their fermentation reactions. Later Eastern and Roman
scholars recognised the importance of legumes and crop residues in
enhancing soil quality.
3.2 Some Important Names in Soil Microbiology and Their

Contributions
(a) Waksman, S.A.:

He wrote the book “Principles of soil microbiology” and encouraged
research in soil microbiology. He studied the Actinomycetes –
Streptomyces and discussed Streptomycin.
(b) Louis Pasteur:

He was responsible for the process of pasteurisation (process of heating
liquids to partially sterilise them). He also researched on microbial
fermentation leading to the delineation of anaerobic metabolism.
(c) Robert Kock:

He pioneered microbial culture technique and showed that
microorganisms were disease – causing agents in his postulate called
Koch’s postulates. Kock’s postulates are as follows:
a) A specific microorganism can always be found with a given
disease.
b) The microorganism can be isolated and grown in a pure culture in
the laboratory.
c) The pure culture will produce the disease when inoculated into a
susceptible host.
d) The microorganism can be recovered from the infected host and
grown again in a pure culture
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SLM 505 MODULE 1
(d) Sergei Winogradsky

He is called “Father of soil microbiology” because of his contributions
to nitrification, anaerobic (N2) nitrogen fixation, sulphur oxidation and
microbial autotrophy. His studies on nitrification and sulphur oxidation
were well noted, leading to the concept of microbial autotrophy where
inorganic substrates are used as source of energy for growth by
microorganisms. He came up with the column for studying sulphur cycle
and investigated microbial growth on carbondioxide (CO2) and
inorganic ions in a process called chemoautotrophy. He also investigated
microbial oxidation of ferrous iron (Fe2+) which is the reduced form of
Fe3+, an essential component of rust.
(e) Beijerinck, Martins

Cultured the 1st symbiotic nitrogen-fixing bacteria that grew in
association with legumes and the 1st non-symbiotic aerobic nitrogen-
fixing bacteria as free living soil organism. These were Rhizobium and
Azotobacter respectively. The non-symbiotic nitrogen fixing bacterium-
Beijerinckia is named after him. He also extracted the first virus from
plants (Tobacco Mosaic Virus – TMV) and developed enrichment
techniques and was credited with saying “Everything is every-where, the
environment selects”.
(f) Lipman, Jacob

Was reported to have found the Department of Soil Chemistry and
Bacteriology at New Jersey Agricultural Experiment Station in 1901. He
is called the “Father of Soil Microbiology in the United States”. He was
interested in the effects of soil organisms on soil fertility and plant
growth. He wrote the book called “Bacteria in Relation to Country
Life”. This was the 1st attempt to popularise the Science of Soil
Microbiology.
SELF - ASSESSMENT EXERCISE

List the important names in soil microbiology and their contributions to
soil microbiology.
3.3 What Is Soil Microbiology?
Soil Microbiology is defined as the study of microorganisms that live in

the soil; their metabolic activity, their roles in energy flow, and
importance in nutrient cycling. The soil science society of America
defines soil microbiology as “the branch of soil science concerned with
soil inhabiting microorganisms, their functions and activities.
3
3.4 Importance of soil microbiology in agriculture
Soil Microbiology is said to be the centre of all life, right from the air
we breathe to food and the water we drink. Understanding of the study
of soil microbiology is important to further understanding agricultural
and environmental impacts on life. In effect, it will furnish you with
knowledge to solve issues related to the functions of other biological
systems in the soil.
4.0 CONCLUSION
From the origin of soil microbiology and the contributions made by

some of the important names in soil microbiology, microorganisms have
had great impact on man. Some of the effects are beneficial while some
are detrimental. On the beneficial side, microorganisms are important in
nutrient cycling and sustainability of life. On the detrimental side, they
may contribute to environmental problems (green-house gases).
Soil microbiologists in this 21st Century, have continued studies in those

areas that have brought us to our present position and encourage us to
step boldly into the future. Hence, soil microbiologists have
concentrated on the opportunities created by these contributions for the
betterment of society through their work. If the past shows sign of good
work, then the future is very promising. May be the solution to the need
for enhanced food production or reduced environmental problem will
cause some microbiologists (perhaps yourself) into the levels of Nobel
Prize winners lie Waksman Selman who was honoured for his work on
antibiotics.
5.0 SUMMARY
Early studies in soil microbiology focused on the study of soil biota and
cycling of nutrients and their availability to agricultural plant. The study
of soil microbiology today, is more of an interdisciplinary study which
involves agricultural production, aquatic and biogeochemical sciences,
microbial biodiversity and climate change. The contributions of
Winogradsky the “Father of soil microbiology” and Lipman the founder
of American Soil Microbiology stands as a landmark in soil
microbiology and has spread throughout the whole world. Their
contributions have improved crop production and given room to sound
use of environmental resources worldwide.
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SLM 505 MODULE 1
6.0 TUTOR-MARKED ASSIGNMENT
1) Define soil microbiology.

2) State some important names in soil microbiology and their
contributions.
3) Discuss the importance of soil microbiology in agriculture
7.0 REFERENCES/FURTHER READING
Brady, N.C.& Weil, R.R. (2002).The Nature and Properties of Soils.

(13thed.).Prentice Hall, Upper Saddle River, NJ.
Eldor, A.P. (Ed.).(2007). Soil Microbiology, Ecology and

Biochemistry.(3rded.). Canada :Academic Press Publications.
Sylvia, D.M., Hartel, P.G., Fuhrmann, J.J. &Zuberer, D.A.

(2005).Principles and Applications of Soil Microbiology.
(2nded.).New Jersey :Prentice Hall, Upper Saddle River.
5
UNIT 2 INTRODUCTION TO SOIL BIOCHEMISTRY
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 What is Soil Biochemistry?
3.2 Importance of Soil Biochemistry in Agriculture
3.3 Relationship between Soil Biochemistry and Soil
Microbiology
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Soil Biochemistry is one of the disciplines of soil science and closely

related with soil microbiology (one of the major disciplines in soil
science). It is the science that deals with the chemical nature and
behaviour of biological living matter in the soil. For this reason, it is
thus referred to as biological chemistry or chemical biology.
In this unit, we will discuss the importance of soil biochemistry in

agriculture and its relation to soil microbiology.
2.0 OBJECTIVES

• define and explain soil biochemistry.
• distinguish between soil biochemistry and soil microbiology
• discuss the role of soil biochemistry in agriculture.
3.0 MAIN CONTENT
3.1 What is Soil Biochemistry?
Soil Biochemistry is defined as a branch of soil science hidden under the

major discipline of soil microbiology in the sense that it deals with the
chemical, nature and behavior of living matter, the transformations
carried out and the energy changes that occur during these biological
transformations. Therefore, the study of soil biochemistry includes the
constituents (substances) that make up the living organisms, substances
produced through their transformation processes and their functions or
6
SLM 505 MODULE 1
chemical activities which involves energy changes. Thus, soil

biochemistry is the backbone of soil microbial functioning.
3.2 Importance of Soil Biochemistry in Agriculture
Soil biochemistry is of great importance in agriculture in the sense that it

is the backbone of soil microbial functioning without which
microorganisms cannot function effectively in the soil. As earlier
mentioned, it includes the chemical compounds that make up part of the
organism living cell or produced by or in the organisms itself. Some of
the biochemical compounds produced by soil microorganisms that have
been observed to be of great importance in agriculture are:
• Enzymes - catalyse chemical reactions during organic matter

degradation (decomposition) and transformations of cycles in
soil.
• Protein synthesis.
• Chalates formation - molecules that bind metal ions to form
complexes and cause nutrient mobilization.
• Toxins formation - like antibiotics beneficial to some soil
organisms in terms of protection from predators or reduces
competition among soil organisms.
• Production of growth regulating substances or hormones like
indole acetic acid (IAA), gibberlins and other substances that
enable the plant to tolerate or withstand salinity problems. From
these biochemical compounds produced you can see that soil
biochemistry helps us to:
• Evaluate the nutritional value of agricultural and livestock
products.
• Biodegrade toxic substances into non-toxic substances (e.g.
breakdown or removal of groundnut toxin called Aflatoxin).
• Serves as food preservative and for processing.
• Helps plants to become disease and drought resistant.
• Helps in the formulation of balanced diet.
• Helps in cell metabolism (the formation and breakdown of cells
tissues).
3.3 Relationship between Soil Biochemistry and Soil

Microbiology
Soil microorganisms and the biochemical compounds they produce play

important role in nutrient transformations and use. This inform,
improves soil quality and soil productivity. The biology of the soil helps
to determine the characteristics of the soil, while microbial
decomposition of soil organic matter enhances soil fertility, growth of
7
plants and microorganisms, improves or sustains the carbon storage of

soil and improves soil structure. From the above discussion and many
more, you can see the relationship between soil microbiology and soil
biochemistry.
SELF-ASSESSMENT EXERCISE
Why do soil microbiology and soil biochemistry matter?
4.0 CONCLUSION
From our discussion in this unit, you can see that soil biochemistry is a
major component of soil microbiology without which soil
microorganisms cannot adequately carryout their metabolic activities.
The biochemical compounds produced by or in these soil organisms
form or make up part of the living cell and are necessary in biochemical
activities such as nutrient transformation and use resulting in soil
productivity. Thus, soil biochemistry is the pillar of soil microbial
functioning, characteristics and dynamics of OM and the
transformations by enzymes and soil organisms.
5.0 SUMMARY
Soil biochemistry is an essential component of soil science that you

cannot do without (that is, cannot be ignored). Soil microbiology cannot
be fully achieved or complete with the biochemical aspect of it. This is
because soil biochemical takes care of all the transformation, function
and energy changes that occurred during these processes. This unit,
therefore looked at the importance of soil biochemistry in agriculture
and its relationship with soil microbiology.
1) Define and explain soil biochemistry.

2) Distinguish between soil biochemistry and soil microbiology.
3) Discuss the role of soil biochemistry in agriculture.
Eldor, A.P. (Ed.). (2007). Soil Microbiology, Ecology and

Biochemistry. (3rded.).Canada: Academic Press Publications.
Hassan, G.D. (2010). Soil Microbiology and Biochemistry.New India

Publishing Agency.
8
SLM 505 MODULE 1
Sylvia, D.M., Hartel, P.G., Fuhrmann, J.J.&Zuberer, D.A.

(2nded.).,Prentice Hall, Upper Saddle River, New Jersey.
9
UNIT 3 THE SOIL HABITAT
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 What is Soil?
3.2 Components of Soil
3.3 Factors Affecting Soil Habitat
3.4 Functions of Soil Habitat
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Soil is defined as a natural medium that supports plant growth on the

earth surface, that is, it is both biologically active and living. It creates a
habitat for microbial growth which feed and supports other plant life.
The microorganisms survive as micro-colonies or biofilms isolated on
mineral or inorganic particles, organic matter and roots depending on
nutrients movements either by mass flow of soil water or diffusion in the
soil. In this unit, you will be looking at the soil as a medium for
microbial growth and development.
2.0 OBJECTIVES
• define soil habitat

• identify some important microbes in the soil habitat
• discuss the importance of soil microbes in the soil habitat.
3.0 MAIN CONTENT
3.1 What is soil?
The soil is a natural medium that supports plant and animal growth and
development on the earth surface and it is biologically active and living.
The microorganisms survive as micro-colonies or biofilms isolated on
mineral (inorganic) particles, organic matter and root depending on
nutrient movements either by mass flow or diffusion in the soil. It is a
heterogenous medium of solid, liquid and gaseous phases that vary in its
physical, chemical and biological properties.
10
SLM 505 MODULE 1
3.2 Components of Soil
The major components of soil are air, water, mineral and organic matter
and consists of three phases – solid, liquid and gas phases. The solid
phase consists of mineral or inorganic and organic matter that make up
the skeletal framework of soils (pore spaces). The pore spaces are
occupied by air and water and can change anytime depending on
weather conditions. They influence the behavior and productivity of
soils. The three phases mix together and encourage simple and complex
reactions within and between soil components for growth and
development of plants.
3.3 Factors Affecting Soil Habitat

Due to the differences in the physical, chemical and biological
properties, the soil environment/habitat is a competitive one. This
competition exists mainly among the major microorganisms in the soil
such as bacteria, actinomycetes and fungi as well as other soil animals
and plant roots due to the stresses or unfavourable conditions in the soil
environment. These unfavourable conditions are classified as biotic and
abiotic stresses.
3.3.1 Biotic and Abiotic Stresses
Biotic stress includes competition from other microbes while abiotic

stress includes physical and chemical properties of the soil habitat.
Competition is as a result of lack of adequate nutrient or substrate,
water, space or growth factors. As a result of competition, some
microbes can secrete allelopathic substances (toxic or inhibitory) like
antibiotics that suppress neighbouring organisms while others are
predatory or parasitic on other microbes.
3.4 Functions of Soil in the Habitat
The soil plays several roles in the soil environment:

a) Support plant growth as a medium for plant roots and supply
nutrient element necessary for growth and development (medium
for plant growth).
b) Control the fate of water in the soil water system – water loss,
use, contamination (pollution) and purification (regulates water
supply).
c) Serves as a recycling medium of nature for raw materials
d) Serves as a medium for microbial existence (habitat for soil
organisms).
e) It is an engineering medium for human environment serving as an
essential building material (baked soil material). Also provides
11
the foundation for road, houses we live in and air-port for air
planes (Engineering medium).
i. List the important soil components and phases of soil habitat.

ii. What is the function of the soil habitat?
4.0 CONCLUSION
From this unit, it can be concluded that:

4) The soil is a medium for plant growth.
5) Competitive inhabitant for soil organisms.
6) Regulates soil water supply.
7) Recycles raw materials in the soilecosystem.
8) Essential building material (engineering medium) for human
environment.
5.0 SUMMARY
The soil habitat is a natural medium that supports plant and animal life
on the surface of the earth and is both active biologically and living. It is
a medium of solid liquid and gas phases. The solid phase consists of
inorganic and organic matter which makeup the skeletal framework. The
pore spaces are filled by air and water and can change at any time
depending on weather conditions. The solid, liquid and gas phases mix
together and enhance simple and complex reactions within and between
soil components for growth and development of plants.
6.0 TUTOR MARKED ASSIGNMENT
1) Define soil habitat.

2) Identify some important microbes in the soil habitat.
3) Discuss the importance of soil microbes in the soil habitat.
Brady, N.C. &Weil, R.R. (2002).The Nature and Properties of Soils.

(13thed).Prentice Hall, Upper Saddle River.
Eldor, A.P. (Ed.).(2007). Soil Microbiology, Ecology and Biochemistry.

(3rded.). Canada: Academic Press Publications, .

(2nded.).Prentice Hall, Upper Saddle River, New Jersey.
12
SLM 505 MODULE 1
UNIT 4 MICROBIAL COMPOSITION OF SOIL
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 What are Soil Organisms?
3.2 Classification of Soil Organisms
3.3 r – k Theory of Colonisationand Succession
3.4 Functions of Soil Organisms
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
A great number and diversity of microbes live in the soil. The microbes
exist as micro-colonies or biofilms isolated on mineral particles, organic
matter and roots depending on the movement of nutrients in the soil. In
this unit, you will be looking at the microbial composition of soil and
the roles the soil organisms play in the ecosystem.
2.0 OBJECTIVES
• explain what soil organisms are

• classify the soil organisms living in soil
• discuss the activities of soil organisms in the soil.
3.0 MAIN CONTENT
3.1 What are Soil Organisms?
Soil organisms are creatures that live most of their lives in the soil. They
include plants, animals, fungi, bacteria, actinomycetes, viruses,
protozoans, nematodes, algae and so on. They are mostly single cells
except for fungi and some small animals. Many of the soil organisms
are small and can only be seen with the aid of a magnifying glass
(microscope). The smallest being the bacteria, followed by
actinomycetes, fungi and then algae. The major groups found in the soil
are shown in the table below:
13
Organism Size (µm) Numbers (g-1 Biomass (kg

soil) wet mass ha-1
soil)
Viruses 0.02 x 0.3 1010 - 1011 300 – 3,000
Bacteria 0.5 x 1.5 108 – 109 300 – 3,000
Actonomycetes 0.5 – 2.0a 107 – 108 500 – 5,000
Fungi 8.0a 105 – 106 10 – 1,500
Algae 5 x 13 103 – 106 5 – 200
Protozoa 15 x 50 103 – 105 1 – 100
Nematodes 1,000b 101 – 102 10 – 1,000
Earthworms 100,000b - -
Adapted from Metting (1993)

a- Diameter of hyphae
b- Length
3.2 Classification of Soil Organisms
a) Soil organisms are classified based on size and ecological

function.
b) Soil organisms are classified based on action or activities.
c) Classification based on growth characteristics.
3.2.1 Classification Based on Size and Ecological Function
Soil animals (fauna) range from macrofauna (earthworms, millipedes)

through mesofauna (mites, springtails) to microfauna (nematodes,
protozoans). The plants (macro and micro flora) include the roots of
higher plants, as well as microscopic algae and diatoms. The macroflora
are largely autotrophs such as vascular plants (feeder root, mosses)
while microflora (root hairs, diatoms, yeast, molds, mildews,
mushrooms, cyanobacteria). The macro being larger than 2mm in width,
meso between 0.1 and 2mm, and micro less than 0.1mm.
3.2.2 Classification Based on Action or Activity
Activities of soil organisms (flora and fauna) are in what we call food
chain or food web. This relationship show how soil organisms are
engaged in plant residue degradation. As one organism eats another,
nutrients and energy are passed from one trophic level to another higher
trophic level. The first trophic level is that of the primary producers
while the second trophic level is the primary consumers that eat the
producers. The third trophic level is the predators which eat the primary
consumers and finally the fourth trophic level are the predators that eat
predators and so on.
14
SLM 505 MODULE 1
3.2.3 Classification Based on Growth Characteristics
Soil organisms are classified on their growth characteristics, nutritional,

ubiquitous and affinity for substrate (nutrient). According to
Winogradsky, organisms that grow very fast (rapidly) when high-energy
containing nutrients are readily available are called zymogenous while
those that colonise the more resistant materials remaining after the
zymogenous attack are known as autochthonous (slow acting)
microflora.
Ohta and Hattori isolated bacteria called Oligotrophs – those that grow
better at low concentration of nutrients while those that grow better at
relatively high concentration of nutrients are called Copiotrophs. Griffin,
classified fungi as primary fungi colonisers – those that have the ability
to metabolise residual substrates of increasing chemical complexity and
recalcitrance while those that colonise residues at the later stages of
decomposition are called secondary fungal colonisers. They are slower
growing and less competitive at growth compared to primary fungal
colonisers. They also produce fewer and more durable spores than
primary fungal colonisers.
3.3 r – k Theory of Colonisationand Succession
Andrews (1984) came up with the possibility of linking microbial

classification based on growth properties with a theory called r – k
Theory of colonisation and succession. This theory suggests that “a
species needs to adopt a different strategy to colonise an environment in
which it is initially present at low density (r – strategy) than to persist in
an environment in which it is already present near to its carrying
capacity (k – strategy)”. The r – strategy place large percentage of their
available energy into reproduction, occupy the niche quickly and are
poorly adapted to environmental stress and periods of low nutrient
availability. Hence, they undergo large changes over time. Examples in
this group are bacteria that belong to the Zymogenous or copiotrophic
traits.
The k-strategy growth and reproduction rate are not affected by limited
resources available and hence have the ability to withstand periods of
low nutrient availability and environmental stress. Examples in this
group are fungi and actinomycetes that belong to the autochthonous or
oligotrophic traits.
3.4 Functions of Soil Organisms
• Breakdown of organic materials and pollutants to water and CO2

(carbon dioxide).
15
• Breakdown or decomposition of organic compounds to simple

inorganic forms in a process called mineralisation.
• Oxidation of reduced mineral element forms example sulphur (S)
to sulphate (SO42-).
• Reduction of oxidised nutrient element forms e.g. NO3- (nitrate)
to N2 (dinitrogen gas)
• Stabilisation of soil humus forms soil aggregate particles and
improve soil structure.
• Buffer the soil pH.
• Nutrient retention and increased water infiltration and water
holding capacity of soil.
• Take part in nutrient cycling/transformation and some act as food
source for other microbes.
List the important soil microbes and their contributions to the soil
habitat.
4.0 CONCLUSION
This unit identified and discussed the major soil organisms and their
roles in the soil ecosystem. Soil organisms are classified based on their
size and ecological function, activities and growth characteristics. They
play important role in nutrient cycling/transformation, soil formation,
breakdown of harmful organic materials to simple forms and in the
improvement of soil fertility and crop productivity. It is therefore clear
that the soil is a habitat for a wide diversity of organisms that are both
beneficial and detrimental to the soil environment.
5.0 SUMMARY
From the soil as a habitat for microbial growth and development, and the
functions or contributions of soil microbes in the soil habitat, microbes
have made great impact on soil environment. Some are beneficial while
some are detrimental. On their beneficial role soil organisms are
essential in nutrient cycling/transformation and sustainability of both
plant and animal life though some contribute to green- house gases due
to their release of methane has which causes green-house effect.
1) Explain what soil organisms are.

2) Classify the soil organisms living in soil.
3) Discuss the activities of soil organisms in the soil.
16
SLM 505 MODULE 1
Brady, N.C.& Weil, R.R. (2002).The Nature and Properties of Soils.

(13thed.).,Prentice Hall, Upper Saddle River.
Eldor, A.P.(ed.) (2007). Soil Microbiology, Ecology and Biochemistry.

(3rded.). .Canada: Academic Press Publications.

Publishing Agency.

(2005).Principles and Applications of Soil Microbiology. (2nd
ed.), New Jersey :Prentice Hall, Upper Saddle River..
17
UNIT 5 PHYSIOLOGY OF MICROBIAL GROWTH
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Growth Characteristics of Soil Organisms
3.2 Growth Curve
3.3 Growth Equation
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Growth is defined as the continuous or progressive development of an

organism. It is seen as the development of some specific organs or the
entire organism. The growth of soil organism is essential for soil
ecosystem function and changes in soil depending on nutrient
availability and adequate physical and chemical conditions.
2.0 OBJECTIVES
• explain what growth is

• discuss the growth characteristics of soil organisms using the
growth curve
• derive the growth equation.
3.0 MAIN CONTENT
3.1 Growth Characteristics of Soil Organisms
Due to differences in nutrient availability in soil, different growth

strategies are required. For instance, under dry surface soil conditions,
biodegradable nutrients may accumulate due to lack of adequate water
to support soil organism’s action but when adequate or sufficient
moisture is added, rapid organism growth which has been shown to take
place. This transient period of nutrient availability can be differentiated
with rhizosphere where constant nutrient supply is available.
18
SLM 505 MODULE 1
Hence the environment provides the organism with the opportunity to

express their growth characteristics and compete for nutrients with their
unique characteristics.
3.2 Growth curve
Under favourable condition of sufficient nutrient supply, organism

growth goes through various phases as shown below:
Adapted from Maier et al. (2009).
After the adaptive or lag phase, the organism enters a period of

unlimited growth. When nutrient supply decreases, toxic metabolites
accumulate and growth slows down. Then growth ceases and followed
by death.
3.3 Growth Equation
At the unlimited growth phases, cell numbers increase exponentially or

double per time interval and this is referred to as doubling time or
generation time (abbreviated td). The number of cells per unit volume
(Nt) after a growth period (t), while at initial population the number of
cells per unit volume is No and number of doubling (n) during the time
interval (t) is expressed as:
Nt = (No) x 2n
Where
t
n=
td
Using linear form of equation
In 2 x t
In Nt = In No +
td
Using logarithm of base 10
19
Log 10 2 x t
Log10Nt = Log10 No +
td
Where
Log 10 2
a) = growth rate constant (N) = slope
td
In 2
N=
2.303 x td
4.0 CONCLUSION
From the physiology of soil organisms, growth is the continuous

development of an organism and could be either a specific organ or the
entire organism depending on the availability of nutrients and the
adequacy of physical and chemical conditions of the soil environment.
The growth of soil organism goes through various phases namely lag,
logarithmic, limited, and stationary and death phases.
5.0 SUMMARY
This unit identified and discussed the various growth stages of soil
organisms depending on nutrient availability and the physio-chemical
soil conditions. After the lag phase, the organism then enters a period of
unlimited growth until nutrient supply decreases and toxic metabolites
accumulate thereby slowing down growth rate and this may eventually
cause growth to cease and finally death of organism.
1) Explain what growth is.

2) Discuss the growth characteristics of soil organisms using the
growth curve.
3) Derive the growth equation.
Brady, N.C. &Weil, R.R. (2002).The Nature and Properties of

Soils.(13thed.), Prentice Hall, Upper Saddle River, NJ.

(3rded.).Academic Press Publications, Canada.
Maier, R. M; Pepper, I. L&Gerba, C. P.(2009).Environmental

Microbiology.Califonia: Academic Press, San Diego.
20
SLM 505 MODULE 1
Sylvia, D.M., Hartel, P.G., Fuhrmann, J. J. &Zuberer, D.A.

(2005).Principles and Applications of Soil Microbiology.(2nded.),
Prentice Hall, Upper Saddle River, New Jersey.
21
SLM 505 MODULE 2
MODULE 2 MICROBIOLOGY OF THE

RHIZOSPHERE AND MICROBIAL
INTERACTIONS
Unit 1 Rhizosphere Soil

Unit 2 Soil Microbial Interactions
Unit 3 Non-Symbiotic VsSymbiotic Associations
Unit 4 Rhizobium Association
Unit 5 MycorrhizalAssociation
UNIT 1 RHIZOSPHERE SOIL
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 What is Rhizosphereand Spermosphere?
3.2 Definitions of Terms in the Rhizosphere
3.3 Factors Affecting Microbial Activity in the Rhizosphere
3.4 Influence of Microorganisms in the Rhizosphere
3.4.1 Beneficial Effects of Microorganisms in the
Rhizosphere
3.4.2 Detrimental Effects of Microorganisms in the
Rhizosphere
3.5 Influence of Plants on the Microorganism
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
As earlier mentioned, the study of the properties and interaction of

organisms in the soil with each other and their environment is called soil
ecology. In the soil, physical and chemical properties of the soil affect
microbial processes or activities. All these affect the overall makeup of
the soil microbial community. These changes in the microbial
community structure can determine the suitability of the soil for crop
production. This unit will introduce you to the topic of soil ecology
with special emphasis on the rhizosphere and the effects of plant and
microorganisms on each other and the soil.
20
2.0 OBJECTIVES
• explain what a rhizosphere is and differentiate it from

spermosphere
• discuss the effect of plants on the microorganism in the
ehizosphere
• discuss the effect of microorganisms in the rhizosphere.
3.0 MAIN CONTENT
3.1 What is Rhizosphere and Spermosphere?
The zone of soil under the influence of living roots is called the
rhizosphere and usually extends more than 5mm from the root and more
importantly, is the area of increased microbial activity because of the
root exudation of substances that affect microbial activity. The area of
increased microbial activity around the seed is called spermosphere. The
term spermosphere arose because the seed is commonly referred to as
the sperm hence; the term spermosphere is in line with the rhizosphere.
The spermosphere can extend up to 10 mm from the seed but distances
up to 20mm have been reported. Seed colonisation is the 1st step towards
root colonisation in the soil. Therefore, spermosphere is the zone of soil
under the influence of the seed.
The rhizosphere and spermosphere have different properties that change

in space and time as the distance from the root or seed increases. These
changes affect the relationship between the plant and the microbial
community. The microorganisms that inhibit the root are known as
endophytes.
The biological and chemical properties of the rhizosphere are different

from those of the bulk soil. For instance, soil acidity may be 10 times
higher (or lower) than the bulk soil. Roots affect nutrient supply by
withholding or withdrawing dissolved nutrients or by solubilizing the
nutrients. As a result of these, roots affect the mineral nutrition of soil
microorganisms just as the microorganisms affect the nutrients available
to the plant roots.
i. The rhizosphere is the zone of increased microbial activity, why?

ii. Spermosphere is an important area of study, why?
21
SLM 505 MODULE 2
3.2 Definitions of terms in the Rhizosphere
The rhizosphere represents a poorly defined zone of soil with a

microbiological gradient in which the maximum effect of roots and
microorganisms are in the soil nearest to the root. The terms outside and
inner rhizosphere are terms used to define the zone of influence.
a) Inner rhizosphere (Rhizoplane)

This is the surface of a plant rot with any adhering soil particles,
Also called Rhizoplane.
b) Outer Rhizosphere
This is the zone beyond the rhizoplane but still under the
influence of plant root. Microscopic and plate count
examinations have revealed presence of microbial activities
around the root and root hairs.
c) R:S ratio
This is the ratio of the number of organisms per gram of the
rhizosphere soil (R) to the number of organisms per gram of the
controlled soil (S).
d) Rhizosphere effect (RE)

Rhizosphere effect is the ratio that expresses the extent to which
the plant roots affect the number of microorganisms. It is usually
greater for bacteria than for other microorganisms inhabiting the
rhizosphere. Fungi and actinomycetes may be abundant but their
active count is usually low.
Distinguish between rhizosphere, rhizosplane and rhizosphere effect.
3.3 Factors affecting microbial activity in the Rhizosphere
1) Organic matter requirements

Plant dead roots and leaves and soil organic matter are energy sources
for a majority of soil organisms especially the heterotrophs. Energy-rich
organic substances including plant root exudates stimulate growth and
activity of microbes. Bacteria respond mostly and rapidly to additions
of freshly introduced or incorporated simple compounds such as starches
and sugars while fungi and actinmycetes respond more to cellulose and
the more resistant compounds. In addition, organic materials left on the
soil surface are dominated by the microbial activity of fungi while
bacteria play larger role when incorporated.
22
2) Oxygen requirements
While most microorganisms are aerobic, some are anaerobic and use
substances like nitrate (NO3-), sulphide (S2-) as their electron acceptors.
Facultative bacteria use either aerobic or anaerobic forms of
metabolism. These forms of metabolism are carried out at same time in
different habitats within the soil.
3) Moisture and temperature

Optimum moisture ranges between -10 to -70 kPa and this is the best for
aerobic microbes while anaerobic microbes prefer waterlogged
conditions, where oxygen supply is limited. Microbial activity is best at
temperatures between 20 – 40 oC. The warmer end of this range
favoursactinomycetes while extreme temperatures kill bacteria and
sometimes temporarily suppress their activity. The only excepts are
cryophilic microbes that strive below 5 oC (biological zero) and
thermophilic that strive beyond 40 oC.
4) Exchangeable calcium (Ca) and pH

Exchangeable calcium (Ca) and pH help to determine which type of
organisms thrive in the soil. High Ca levels and near-neutral pH
generally result in the largest and most diverse bacterial populations
while low pH (acidic conditions) favour fungi. This is why fungi
dominate forested soils.
3.4 Influence of microorganisms in the Rhizosphere
3.4.1 Beneficial effects
The microorganisms in the rhizosphere may have beneficial or

detrimental influence on the development of plants. This is because,
since microbes are so closely related to the plant root systems, any
beneficial or toxic substance produced can cause an immediate and
profound effect on the microorganism. Therefore, microbes are
important to plant productivity and ecological functioning of soils.
1) Organic material decomposition

This is the most important contribution of microorganisms to higher
plants in the rhizosphere. In this process, dead leaves, roots and other
plant tissues are broken down (degraded) converting the organically held
nutrients to inorganic (mineral) forms available for plant uptake. Soil
microbes also assimilate wastes from animals and other organic
materials. Some of the new compounds produced help to stabilize soil
structure and others contribute to humus formation.
23
SLM 505 MODULE 2
2) Breakdown of toxic compound

Many organic compounds toxic to plant and soil organisms which find
their way into the soil (as metabolic by-products) are broken down into
non-toxic compounds by those organisms that produce enzymes that use
these toxins as food. Some of these toxins are xenobiotic (artificial) and
may resist attack by microbial enzymes. Bacteria and fungi are
important in maintaining a non -toxic soil environment. The
detoxicifying activity of soil microbes is greatest on soil surface where
microbial numbers are concentrated in response to greater availability of
organic matter and oxygen.
3) Inorganic transformations
Inorganic transformation is of great importance to the functions of soil
ecosystem. Nitrate (NO3-), sulphate (SO42-) and to a lesser extent
phosphate (PO4-) ions are present in soil due to microbial action.
Bacteria and fungi takeup some of N, P and S in the organic materials
they degrade. Excess of these nutrients are then excreted into the soil
solution in organic forms. Also nematodes and protozoa that feed on
them takeup these nutrients. Other essential nutrients like Fe and Mn
(micronutrients) are determined largely by microbial action. In well-
drained soil (aerobic) they are oxidized by autotrophic organisms to
higher valency state making them insoluble. This keeps Fe and Mn
mostly in insoluble and non-toxic forms even under fairly acid
condition. If such oxidation did not occur, plant growth would be
adversely affected due to the toxic quantities of these elements in
solution.
4) Nitrogen fixation
The fixation of atmospheric nitrogen that cannot be used directly by
higher plants is one of the most important microbial processes in soils.
For instance, actinomycetes (Frankis sp.) fix major amounts of nitrogen
in forest ecosystems, cyanobacteria in flooded rice paddies and wetlands
and rhizobia in agricultural soils in association with legume root
nodules. The greatest amount of N fixed by these organisms occurs in
root nodules.
5) Rhizobacteria
The rhizosphere soil and rhizophane support large population of
microorganisms. Bacteria that live in this zone are called rhizobacteria.
Many of them are beneficial to higher plants called the plant growth
promoting rhizobacteria. Because the root surface is almost covered
with bacterial cells, little interaction between the soil and plant root take
place and this cannot be done without some microbial influence. Many
rhizobacteria enhance nutrient uptake or hormonal stimulation while
some damage plants by invading the root cells and live as parasites.
Other rhizobacteria inhibit root growth and function, thereby causing
24
stunting, wilting, foliar discolouration, nutrient deficiency and even

death of plants. Buildup of deleterious rhizobacteria cause yield declines
especially under long-term monocultures, even in planting new trees in
old orchanrds. Their main beneficial effect is in weed control, thus weed
scientists hope to reduce weed seed germination and seedling growth,
thereby reducing the use of herbicide.
6) Plant protection
Some soil organisms attack higher plants while others protect plant roots
from parasites and pathogen invasion.
3.4.2 Detrimental Effects of Microorganisms in the

Rhizosphere
1) Microorganisms also require some anions and cations for their

own growth and development leading to nutrient immobilization.
For instance, when absorption of soluble inorganic phosphate is
affected, immobilization of Mn, Fe, Zn, K is stimulated.
2) Some microbes have injurious effect on higher plants as plant
parasites or by producing certain toxic substances.
3.5 Influence of Plants on Soil Microorganism
The activities of plant roots greatly affect the soil chemical, physical and
biological properties depending on the soil type and plant species. The
effect of plants on organisms in the soil are as follow:
1) Increase soil aggregate stability

The plant root hairs increase root surface area available to absorb water
and nutrient from soil solution, thereby encouraging soil aggregate
stability. The root exudate supports large community of microorganisms
which further help to stabilize soil aggregates.
2) Increase humus content of soil (SOM)

When the dead plant parts decompose, they increase soil humus both at
the surface and subsurface layers of soil. Three types of organic
compounds are released at the soil surface:
a) Low molecular-weight organic compounds secreted by root cells,

e.g. organic acids, sugars, amino acids and phenolic compounds
which exert growth stimulating or regulating effects on plants and
soil microbes.
b) High molecular – weight mucilages secreted by root-cap cells and
epidermal cells e.g. mucigel.
c) Cells from rootcap and epidermis (slough offs, root materials)
25
SLM 505 MODULE 2
All these are called rhizodeposition.
3. Microorganisms are affected by plant root respiration which

alters the pH or availability of some inorganic nutrients due to the
release of CO2. The pH of the rhizosphere is however more than
the surrounding soil when roots are assimilating NH4+
(ammonium ion) but higher when NO3- (Nitrate) is being taken
up.
4. Root penetration improves soil structure which favour microbial
oxidation.
5. Increase in the population of denitrifying bacteria due to the
presence of NO3- which enhance N2 and NO (nitrous oxide)
release by plant growth.
6. Presence of certain plants reduces abundance of nitrifying
organisms.
7. Increase in the abundance of celluloytic microorganisms due to
response to cellulose produced from slough-off root materials.
These microbes degrade cellulose providing carbonaceous
substrate for some microorganisms.
What role does plant exudates in the rhizosphere?
4.0 CONCLUSION
The rhizosphere is the zone of soil under the influence of living roots
usually extends more than 5mm from the root and spermosphere is the
zone of soil under the influence of the seed. Soil microorganisms are
affected by organic compounds released from plant roots or seed and
these compounds alter the microbial community structure, increase
microbial population, activity and interactions among microbes, plant
and the soil. The microorganisms in the rhizosphere can exert beneficial
or detrimental effects in plant, thereby affecting plant productivity.
5.0 SUMMARY
Rhizosphere which is the zone of soil under the influence of living roots
is the area of increased microbial activity because of the root exudation
substances, that affect microbial activity.
From the study in the unit, soil microorganisms play important role in
plant growth and development and this could be positive or negative,
likewise plants exert great effect on soil microorganisms due to their
exudate excretion which alter the soil chemical and physical properties
of the soil.
26
1) Explain what a rhizosphere is and differentiate it from

spermosphere.
2) Discuss the effect of plants on the microorganism in the
ehizosphere.
3) Discuss the effect of microorganisms in the rhizosphere.
Brady, N.C. & Weil, R.R. (2002).The Nature and Properties of Soils.
(13thed.).Prentice Hall, Upper Saddle River.
Eldor, A.P. (Ed.). (2007). Soil Microbiology, Ecology And Biochemistry.

(3rded.).Canada.: Academic Press Publications.

(2nded.).New Jersey:Prentice Hall, Upper Saddle River.
27
SLM 505 MODULE 2
UNIT 2 SOIL MICROBIAL INTERACTIONS
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Types of Interactions
3.1.1 Positive Interactions
3.1.2 Negative Interactions
3.2 Microbial Succession
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Due to the limited nutrient supply and environmental problems in the

soil, microorganisms compete within and among themselves for the
limited nutrient supply, space, time and water supply in other to survive
the adverse soil conditions. In other to mitigate these adverse soil
problems, soil microorganisms interact with themselves and with other
organisms in the soil. Many of these interactions occur through some
biochemical signaling in the rhizosphere. These interactions are seen on
the basis of whether one or both organisms gain benefit from the
association. The study of these interactions among microorganisms and
their environment is called soil ecology.
Biochemical Signaling
This is the information passed within and among microorganisms that
are created and transmitted through the production of biochemical
compounds by the microorganisms. These biochemical compounds are
instruments used by the soil microorganisms to carry out their functions
essential for plant growth, development and nutrition.
2.0 OBJECTIVES
• distinguish the various types of interactions among soil

microorganisms
• classify them into beneficial (positive) or detrimental
(negative) interactions
• explain microbial succession.
28
3.0 MAIN CONTENT
3.1 Types of interactions
A number of possible interactions that may occur between two species

are:
1) Commensalism
2) Neutralism
3) Symbiosis (mutualism)
4) Proto-cooperation (synergism)
5) Competition (Antagonism)
6) Ammensalism
7) Parasitism and predation
3.1.1 Positive Interactions
1) Commensalism
This is an interaction in which one population or microorganism benefits
from the interaction and the second remains unaffected. This is the basis
for nitrification in nitrogen cycle. For instance, the ammonia-oxidising
bacteria (Nitrosomonassp.) transform NH3 into product (Nitrate) that is a
substrate for the nitrite-oxidising bacteria (Nitrobacter sp.).
2) Neutralism
This is an interaction in which the two microorganisms (populations)
behave entirely independent of each other.
3) Protocooperation (synergism)
In this ineraction, both populations of microorganisms benefit from the
association but the interaction is not compulsory for their existence or
performance in the environment. For instance, in anaerobic soils, the
methane producing bacteria benefit from the acetate and hydrogen gas
produced by the fermentative bacteria while the fermentative bacteria
benefit by the lowering of the hydrogen gas and acetate concentrations
by methane producing bacteria thereby allowing them to put together
heat changing (thermodynamically) biochemical reactions to cell
growth.
4) Symbiosis (mutualism)
This interaction occurs between specific organisms rather than
populations. In this interaction both microorganisms benefit from the
association and cannot survive (grow) without the other in the
association.
This association can be found between:
29
SLM 505 MODULE 2
a) Bradyrhizobium or Rhizobium with leguminous plants.

b) Actinomycetes (Frankia sp.) with plants (Actinorhizal).
c) Algae and fungi (Lichens).
d) Fungi with roots of higher plants (mycorrhizae).
e) Bacteria within protozoan cells.
f) Protozoan in underground termites (similar to bacteria in intestine
of ruminants).
g) Some ants, beetles and termites grow some fungi (the insects
provide the fungi with nutrients for growth such as dead plant
debris (roots, leaves) and faeces while the insect feed on the
fungal biomas).
3.1.2 Negative Interactions
1) Predation and Parasitism

This is an interaction in which there is direct attack of one organism.In
another, in this interaction, one population has a negative effect on the
size of another population by feeding on them and reducing their
number.For instance, nematodes and protozoa feed on bacteria and
fungi.
2) Competition (Antagonism)
This is an interaction in which there is a suppression of one organism as
the two species struggle (compete) for limiting quantities of nutrients,
water, oxygen and other needed requirements thereby having a negative
effect on each other. Example: Heterotrophic microorganisms and
ammonia-oxidising bacteria (Nitrosomonas) compete for ammonium ion
(NH4+).
3) Ammensalism
This is an interaction in which one species is suppressed by toxins
produced by the second species and the second species is not affected,
thereby gaining a competitive advantage.
Examples:
a) Many fungi and bacteria produce antimicrobial growth
substances that inhibit other organisms.
b) Sulphur-oxidisingmicroorganism causes soil acidification, which
affect acid – sensitive organisms like streptomyces sp.
3.2 Microbial Succession
This is an important series of change in microbial populations in the soil

environment, resulting in the arising of a climax community. Microbial
succession takes place because when organisms grow, they alter the soil
environment around them giving way for the development of other
30
different microbial populations. The initial populations that respond to

the addition of freshly introduced carbonaceous materials are called
primary microflora. As theprimary microflora grow, they alter their
environment and the carbonaceous materials thereby changing the
products into microbial biomass and metabolic waste products. Then
the secondary microflora takes over which feeds on the products of the
primary microflora. This results in a progressive change in microbial
populations as substrates are broken down under different soil
environmental conditions such as pH, oxygen and Eh (redox potential).
4.0 CONCLUSION
Nutritional limitations and environmental conditions of the soil as well

as time and space are the causes of microbial interactions in the soil, in
order for soil microorganisms to mitigate (solve) these adverse soil
problems. These interactions mostly occur through biochemical
signaling. The interactions that have been reported to occur are
commensalism, neutralism, photocooperation, symbiosis, competition,
ammensalism, predation and parasitism. The 1st four types of
interactions are positive interactions while the rest others are negative
interactions. However, soil physical and chemical properties as well as
carbonaceous materials introduced into the soil put together affect soil
microbial metabolic activity and determine microbial community
structure.
5.0 SUMMARY
From the discussion in this unit, the types of interactions within and
among soil microorganisms can be summarized as follows in the table
below:
Type of interaction Effect of interaction within and among soil

microorganism
1st population 2nd population
Commensalism + 0
Synergism + + or 0
(photocooperation)
Mutualism (symbiosis) + +
Competition - -
(Antagonism)
Predation and Parasitism - +
Ammensalism - + or 0
Note
+ means positive effect, - means negative effect, 0 means no effect
(Reproduced from Sylvia et al, 2007).
31
SLM 505 MODULE 2
1) Distinguish the various types of interactions among soil

microorganisms
2) Classify them into beneficial (positive) or detrimental
(negative) interactions.
3) Explain microbial succession.

(13thed.), Prentice Hall, Upper Saddle River, NJ..


(2005).Principles and Applications of Soil
Microbiology.(2nded,).Prentice Hall, Upper Saddle River, New
Jersey.
Atlas, R.M. &Bartha, R. (1981).Microbial Ecology: Fundamentals and

Applications. Addison-Wesley Publishing Company. Reading,
Massachusetts.
Lynch, J.M. &Hobbie, J..E. (1988).Microorganisms in Action: Concepts

and Application in Microbial Ecology. Blackwell, Oxford.
32
UNIT 3 NON-SYMBIOTIC VS SYMBIOTIC

ASSOCIATION
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Biological Nitrogen Fixation (BNF) and Types
3.2 Non-Symbiotic Nitrogen Fixation
3.3 Mechanism (Process) of Nitrogen Fixation
3.4 Symbiotic Nitrogen Fixation
3.4.1 Cross Inoculation Groups
3.5 Nodule Formation and Effectiveness
3.5.1 Nodule Formation
3.5.2 Nodule Effectiveness
3.6 Factors Affecting Symbiotic Nitrogen Fixation
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Nitrogen is an essential element for all living organisms not just soil
microorganisms. It is a major component of protein (amino acids).
Nitrogen in the atmosphere is transformed into the plant available forms
in a process called biological nitrogen fixation (BNF). This process is
carried out by the bacteria – Rhibobium and Bradyrhizobium in a
mutualistic association with legumes forming root nodules.
Biological nitrogen fixation occurs as non (free living) symbiotic

fixation and symbiotic nitrogen fixation. Free-living (not plant
associated) and symbiotic plant associated – root nodule symbiosis).
2.0 OBJECTIVES
At the end of this unit, you shouldbe able to:
• discuss BNF and the types of BNF

• understand cross inoculation group
• discuss or explain the process of nodule formation and
effectiveness
• explain the factors affecting symbiotic nitrogen fixation.
33
SLM 505 MODULE 2
3.0 MAIN CONTENT
3.1 Biological Nitrogen Fixation (BNF) and Types
Biological nitrogen fixation is the process by which atmospheric

nitrogen is converted into plant available forms. This process is brought
about by either the free living bacteria (blue-green or cyanobacteria) –
non symbiotic fixation or by Rhizobium or Bradyrhizobium in
symbiotic fixation with higher plants.
3.2 Non-Symbiotic Nitrogen Fixation
An example of this non-symbiotic nitrogen fixation is the association or

interaction between algae (green or blue-green algae) and fungi
(lichens). In this interaction the algae are known as the phycobiont while
the fungi are known as the mycobiont (Ascomycetes and
Basidomycetes). The algae (phycobiont) benefits from the protection
provided by the fungi which envelopes the algae and protects it from
environmental stress. The fungus (mycobiont) gains by making use of
the carbon dioxide (CO2) fixed by the algae.
The free living heterotrophic nitrogen fixing bacteria are divided into
three groups namely:
1) Obligatory aerobes
Examples are: Azotobactervirinlandi, A. biejerinkia) and Biejerinkia

spp., Pseudomonas spp., Norcaclia sp., found mainly in tropical acidic
soils.
2) Facultative anaerobic bacteria
Examples are the Bacillus sp. (Bacillus polymyxia, B. mercerous, B.

circulars), and those belonging to the Enterobacterium family
(Klebsiella, pneumonia, Enterobacter cloacae, Escherischiatrictly
anaerobic bacteria).
3) Strictly anaerobic bacteria
Example: Clostridium pasterClostridiumpasterianium, Desulphuruibro,

methano bacterium chlorobiumand chromatium.
Azotobactersp are the most active in this type of symbiosis. They can fix
about 5 – 20 µg of N and 1g of sugar; hence do not contribute much to
the soil. The blue-green algae also called cyanobacteria fix N under
34
waterlogged conditions (e.g. sugarcane plantations) and fix about 15 –

20 kg N.
Some of the factors affecting the non-symbiotic nitrogen fixers are:
4) C:N ratio
5) Oxygen content
6) Molybdenum content
7) pH
8) Ca2+
9) Excess Fe and Al
10) Temperature level
3.3 Mechanism (Process) of Nitrogen Fixation
The mechanism through which BNF proceeds and the enzyme

responsible for the reaction is shown in the overall reaction below:
nitrogenase
N2(g)+ 8e- + 8H+ + 16Mg ATP 2NH3 + 16 MgADP + 16 Pi
+ H2
enzyme
Where,
N = Nitrogen, NH3 = Ammonia, H+ = Hydrogen ion,
ATP = Adenosine Triphosphate,
ADP = Adenosine Diphosphate, Pi = inorganic phosphorus
From the reaction equation one molecule of nitrogen gas is reduced to

two molecules of ammonia using energy to carry out the reduction
process. It is estimated that 12 moles of Mg ATP are required for one
mole of N2 (gas) to be reduced to 2 moles of NH3 (ammonia). The
enzyme responsible for carrying out this reaction is called nitrogenase
and consists of two proteins namely:
11) Iron-protein (Fe-protein) (Azoferrodoxin or Azofer) also known
as dinitrogenasereductase.
12) Molybdenum – Fe protein (Molybdo-ferredoxin/Azofermo called
component 1) also known as dinitrogenase
These nitrogenase proteins (Fe-protein and Mo-Fe protein) are Fe-

sulphur components and the Fe protein is the smaller of the two
proteins. The Fe protein is inactivated by oxygen. The molecular weight
of Fe protein ranges between 50,000 – 70,000 while Mo –Fe protein is
inactivated by O2 but not as quickly as Fe protein. They need Mg2+ ion
to be active and also inhibited by ADP. From the mechanism of
nitrogenase enzyme; it is seen that:
• The Fe protein accepts electrons from ferredoxin and binds to
two Mg ATP and then transfers electrons to Mo Fe protein.
35
SLM 505 MODULE 2
• Fe protein and Mo - Fe protein then forms a complex, the

electron is transferred and 2 Mg ATP are hydrolysed to 2 Mg
ADP + Pi (in organic phosphate).
• Fe protein and Mo - Fe protein dissociated and the process is
repeated.
• When nitrogenase has gotten electrons enough, it binds one N2
molecule, reduces it to form NH4+.
• The Mo-Fe protein than accepts more electrons from Fe protein
to repeat the cycle.
3.4 Symbiotic Nitrogen Fixation
Symbiotic nitrogen fixation is a mutualistic (symbiotic) interaction

between two organisms rather than between populations. Both
organisms benefit from the association and most times,no organism can
grow in the absence of the other. In this association, the microorganism
is the prokaryotic organisms (Rhizobium, Bradyrhizobium, Klebsiella,
Nostoc or Frankia) and the plant a eukaryotic usually photosynthetic
(leguminuous or non-leguminous plant, water fern or liverwort). Plants
are the primary source of reduced carbon for the soil microbial
community, and the plant growth is also linked by the availability of N
and P. Therefore, plants solve this environmental adverse conditions or
problems by forming associations with various soil microorganisms.
Two examples of agricultural importance in association are:
13) Fungi and roots of higher plants
14) Rhizobium with legumenuous plants
The amount of nitrogen fixed in legumes vary and could go up as high

as 600 kg N fixed per hectare (600 kg Nha-1).
3.4.1 Cross Inoculation Groups
Various legumes prefer certain rhizobia strains thus rhizobia are grouped
based on their nodulation but not on effectiveness. Some legumes (e.g.
soybean) are promiscuous and can form nodules with more than one
type of rhizobia. Therefore, cross-inoculation grouping is used to
understand rhizobium grouping better. Cross – inoculation group
therefore, refers to a collection of leguminous species that can form or
develop nodules when exposed to bacteria gotten from the nodules of
any member of that plant group. About 20 cross inoculation groups have
been established but only about eight (8) of them have achieved
prominence. Some of the selected cross-inoculation groups and their
legume host are given in the table below:
36
Cross Rhizobium Host genera Legumes

inoculatio sp. included
n group
1) Alfalfa R. melilotus Medicago Alfalfa,Sweet
gp Melilotus clover,
Trigonella Fenugreek
(masala)
Clover gp R. trifoli Trifolium Clovers
Pea gp R. PisumVicia Pea,VetchSweet
leguminosaru Latyrus pea lentil
m Lens
Bean gp R. phaseoli Phaseolus Beans
Lupine gp R. Lupini Lupinusornithopus Lupines,Serradel
la
Soybean R. japonicum Glycine vigna Soybean
gp
Cowpea Cowpea Vigna,LespedezaCrotol Cowpea
gp Bradyrhizobi aria, ArachisPhaseolus, Lespedeza
um Pueraria crotalaria
Peanut
Lima bean
Kudzu
Fast lotus R. Isolates Lotus,Leucaena
and
Leucaena
gp
Based on Alexander, M. (1977).
3.5 Nodule Formation and Effectiveness
3.5.1 Nodule Formation
In the Rhizobium-legume symbiosis, the nodule bacteria infect the host

plant (legume) by entering the host through the root hairs. This first step
involves the release of biochemical compounds that produce signals in
the rhizosphere that stimulate the nodule bacteria. These biochemical
compounds cause increase in the population of the rhizobium in the
rhizosphere. The biochemical compounds excreted by the legume host
roots stimulates only the bacteria of the specific cross inoculation group.
In the root hairs, infection threads are formed resulting in the curling of
the root hairs (evidence of infection). The infection thread provides
enterance for the rhizobia into the plant tissue resulting in the
development of nodules. Rapid multiplication of the plant cell occurs.
The bacteria are released into the cytoplasm where they multiply for a
37
SLM 505 MODULE 2
short period. The host then builds a layer of cell in which an extensive
vascular system is formed containing the rhizobia and the cutile area.
The rhizobia after multiplication converts into non-motile, non-growing
cells called bacteriods. Bacteriods vary in size and shape. These
bacteriods are essential for fixation to take place. Alongside the
bacteriods, legume haemoglobin which is important in the fixation of N
is developed and this gives the effective nodule its pink colour. The
legume haemoglobin changes to give greenish colour when ageing. The
size, shape and location of nodule also vary but to a limited extent the
bacteria strains. Legume plants with tap root (soybean, cowpea) have
larger but fewer nodules while those with branched root (groundnut)
have smaller but more nodules. The diagrams below show the structure
of a nodule and bacteriods.
Adapted from Bala (2012)
3.5.2 Nodule Effectiveness
Nodule effectiveness is the ability of the symbiotic system when formed

to take up (assimilate) molecular N. Different legumes combine with
Rhizobia in their symbiotic association to produce nodules and fix N
and their ability to nodulate and fix N varies. Some combinations
(associations) produce long lived nodules which fix N at high rate.
These are the highly effective associations. On the otherhand, when no
detectable N is fixed by the nodule, it is termed ineffective and may
become parasitic by reducing the yield of the nodulating plant.
Differentiate between nodule effectiveness and ineffectiveness.
3.6 Factors Affecting Symbiotic Nitrogen Fixation
Several factors have been observed to influence nodulation and

symbiotic N2 fixation. These factors may affect negatively the
rhizobium population and survival rate, including the legume host plant.
These factors include:
38
15) High temperature – kills rhizobia and reduces nodulation.

16) Acidity – Limit rhizobial growth and persistence.Acidity reduces
nodulation and this is common in acid soils probably because few
rhizobia persist and acidity affects rhizobia attachment to their
host. Fast growing rhizobia are more sensitive than the slow-
growing Bradyrhizobia though, few low pH tolerant strains exist.
17) Drought – kills rhizobia and reduces BNF (Biological nitrogen
fixation).
18) Waterlogging – Rhizobium do well in waterlogged soils
(anaerobes) but legumes growth and development are affected
due to deficiency (lack) of oxygen and accumulation of toxic
minerals.
19) Salinity and alkalinity – legume are more sensitive to salinity and
alkalinity than rhizobia. Salinity reduces nodulation while
alkalinity limits the availability of micronutrient in the soil,
thereby affecting plant growth and N2 fixation.
20) Mineral nutrients – Mineral nutrient deficiency affects specific
functions in nodulation and N2 fixation. Mineral nutrient
deficiency will cause yellowing (chlorosis). Ca, P and
micronutrient (Mo, Co, B and Fe) reduces nodulation and N2
fixation. Mo causes nodule ineffectiveness; B and Zn reduce
nodule number and size; Co delay nodulation; Cu reduce BNF
and Fe reduce nodule initiation and development.
21) Extent of nodulation and rhizobium effectiveness.
22) Adequate carbohydrate (food) supply.
4.0 CONCLUSION
Biological nitrogen fixation results from the infection of host roots by

rhizobia as a result of nodule development, function and senescence.
The process of nitrogen fixation is brought about by either free-living
Bacteria (non-symbiotic fixation) or by Rhizobium or Bradyrhizobium
(symbiotic fixation) with higher plants. Nitrogenase enzyme is the
enzyme responsible for carrying out the process of nitrogen fixation and
has two components namely, the Fe protein and the Mo-Fe protein. The
rhizobia are grouped based on their cross inoculation group (nodulation)
but not on effectiveness. The nodules formed could be either effective
(pink in colour) or ineffective (greenish in colour). Effective nodules are
those that have the ability to fix dinitrogen while the ineffective nodules
are those that form nodules but do not fix dinitrogen in soil. Several
physical and chemical factors such as temperature, acidity, drought,
waterlogging, mineral nutrients, salinity and alkalinity, carbohydrate
supply and nodulation and rhizobia effectiveness was reported to affect
symbiotic nitrogen fixation.
5.0 SUMMARY
39
SLM 505 MODULE 2
This unit dealt with the ability of legumes to fix dinitrogen in

association with rhizobium. It also discussed that symbiotic nitrogen
fixation could be carried out by either free-living Bacteria in non-
symbiotic association or by rhizobium in the symbiotic association. The
process of nitrogen fixation was discussed including the cross
inoculation groups of rhizobia. Nodule effectiveness and ineffectiveness
was introduced noting the importance of nitrogenase enzyme and
legume haemoglobin in nitrogen fixation.
1) Discuss BNF and the types of BNF.

2) Explain cross inoculation group.
3) Discuss or explain the process of nodule formation and
Effectiveness.
4) Explain the factors affecting symbiotic nitrogen fixation.
Alexander, M. (1991).Introduction to Soil Microbiology.(2nded) .Wiley,

New York.
Bala, A. (2012). Lead Farmer Training in Biological Nitrogen Fixation

and Grain Legume Enterprise.Adapted by AbdullahiBala for the
Training of Trainers and Lead Famers within the N2Africa West
Africa Outreach Project. 154pp.

(13thed)., Prentice Hall, Upper Saddle River, NJ..
Eldor, A.P. (Ed.) (2007). Soil Microbiology, Ecology and Biochemistry.


(2005).Principles and Applications of Soil Microbiology.(2nded.),
Prentice Hall, Upper Saddle River, New Jersey.
40
UNIT 4 RHIZOBIUM-LEGUME ASSOCIATION
CONTENT
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 The Rhizobium Bacteria
3.2 Life-Cycle of Rhizobia
3.3 Rhizobium and Legume Roots
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
In the soil habitat, there are soil organisms which interact with
leguminous plants to form symbiotic associations, also called
mutualistic interactions. These soil organisms are called Rhizobia.
Leguminous plants form mutualistic symbiosis with root nodule bacteria
mostly of the genera Bradyrhizobium and Rhizobium. In this unit, we
will discuss the importance of Rhizobium bacteria in the soil, its life
cycle and give brief explanation of its association on legume plant roots.
2.0 OBJECTIVES
At the end of this unit, you shouldbe able to:
• discuss the life cycle of Rhizobium

• discuss its role in soil and on plant roots.
3.0 MAIN CONTENT
3.1 The Rhizobium Bacteria
Legumes have a long history of use in agriculture especially in

association with the root nodule bacteria (Rhizobium). Not all legumes
are nodulated by the bacteria rhizobia. They live in the soil along with
other soil microorganisms without their host plant (legume). While in
soil, they are saprophytes normally referred to as native rhizobia. They
range from zero to thousands per gram of soil depending on the soil
conditions.
41
SLM 505 MODULE 2
3.2 Life-Cycle of Rhizobia
As previously mentioned, rhizobia live in the soil alone with other soil
microorganisms (without the legume host) as saprophytes. This stage is
called the saprophytic phase. They persist in the soil due to the presence
of decaying root nodules from previous symbiosis or in the presence of
non-host plants. Then when in association with the legume host, the
infective phase occurs after several steps in the rhizobia life cycle. This
phase is affected by environmental conditions such as soil salinity and
low pH. Then the symbiotic phase takes place after the infective phase.
This phase is the development and root nodule function stage in the life
cycle of the rhizobia. It is also influenced by harsh environmental
conditions that affect the host plant. In the soil, the native rhizobia
population is high and there is always competition when new inoculant
of rhizobia is introduced.
3.3 Rhizobium and Legume Roots
The association between the Rhizobium and legume roots is called

symbiotic or mutualistic interaction. Both the Rhizobium and the plant
(legume) root benefit from the association and occasionally the partners
cannot grow in the absence of the association. The plants are the source
of reduced carbon for the rhizobia. The plant growth is often affected or
limited by the availability of N and P. Therefore, in order to solve this
problem, plants form association with various soil organisms such as
rhizobia. The association is mostly with the genera Bradyrhizobiumand
Rhizobium. The rhizobia invade the legume through the root hairs or by
passage between the epidermal or cortical cells. As a result of some
organic bio-chemical compounds released, signals are passed between
the rhizobia and the legume and root nodule are formed. The rhizobia fix
atmospheric dinitrogen (N2) gas into ammonia, which the legume plant
supplies the rhizobia (bacteria) with reduced carbon as energy source for
metabolic processes which includes nitrogen fixation. Because of this
interaction, legume plants can grow in extremely mineral nitrogen
deficient soil condition.
4.0 CONCLUSION
The rhizobium and Bradyrhizobium interact with the legume plant in a

symbiobic (mutualistic) association. The rhizobia are special soil
microorganisms that are beneficial to the legumes. They can live in the
soil alone (Saprophytes) or in the legume root nodules. The rhizobia life
cycle involves three phases namely saprophytic, infective and symbiotic
phases. In the symbiotic phase, atmospheric dinitrogen (N2) gas is fixed
by the rhizobia in the legume root nodule which the plant assimilates
42
into amino acid, while the plant supplies the rhizobia with reduced
carbon as energy source. Because of this association, the legume plant
can grow in extreme nitrogen deficient soil.
5.0 SUMMARY
From the discussion in this unit, it can be seen that rhizobia are special
bacteria having three stages or phases in it life cycle. It can exist in the
soil alone as saprophytes or in association with legumes in root nodules
where atmospheric dinitrogen gas is fixed in a symbiotic association.
They are specific in their association with legumes. In the soil, the
native rhizobia population is high and there is always competition when
new species or inoculants of rhizobia are introduced.
1) Discuss the life cycle of Rhizobium.

2) Discuss its role in soil and on plant roots
.
Alexander, M. (1991).Introduction to Soil Microbiology. (2nded.).New

York :Wiley,.
Bala, A. (2000). Lead Farmer Training in Biological Nitrogen Fixation

and Grain Legume Enterprise.Adapted by AbdullahiBala for the
Training of Trainers and Lead Famers within the N2Africa West
Africa Outreach Project.

Soils.13thed,). Prentice Hall, Upper Saddle River, NJ.
Eldor, A.P. (Ed.) (2007). Soil Microbiology, Ecology and

Biochemistry.3rded.). Canada: Academic Press Publications,

(2nded.).New Jersey: Prentice Hall, Upper Saddle River,
43
SLM 505 MODULE 2
UNIT 5 MYCORRHIZA ASSOCIATIONS
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 What is Mycorrhizae
3.2 MycorrhizaAssociation
3.3 Types of MycorrhizaFungi
3.4 Benefits of Mycorrhiza Fungi in Ecosystems
3.5 Mechanism of Nutrient Uptake
3.6 Factors that Affect Mycorrhiza Fungi
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Another group of rhizosphere microorganisms which form symbiosis

with roots of higher plants is mycorrhiza fungi. A mycorrhiza forms
when the right fungus invades a plant root in a process that is similar to
the infection by pathogenic fungi. In this association, the fungus and the
plant co-exist so that both parties benefit from the relationship. In this
unit, you will see the benefits of mycorrhiza symbioses, types of
mycorrhiza fungi, the mechanisms of nutrient uptake and the factors
affecting mycorrhiza fungi.
2.0 OBJECTIVES

• discuss mycorrhiza association
• explain their benefit in agroecosystem
• identify mechanisms of nutrient uptake especially P.
• discuss the factors affecting mycorrhiza fungi.
3.0 MAIN CONTENT
3.1 What is Mycorrhizae?
The term mycorrhizae mean “fungus root”. It is an association where

certain fungi invade plant roots and form an extensive network of
hyphae that penetrate either between or into the cortical cells and into
44
the soil environment. This association is called mycorrhiza (that fungi

and the root of higher plant).
3.2 MycorrhizaAssociation
In this association, the fungi act as an extension of the plant root system
helping the plant root to assimilate (take up) nutrients especially
phosphorus (P) that is slightly mobile in soil. Due to the low solubility
of P, the availability of P in the soil solution is limited. As a result of
this problem the fungi helps the plant in the uptake of nutrients from soil
solution by penetrating the soil in search of P and other nutrients
through the process of active transport mechanism. The fungal hyphae
then release the nutrients and the plant roots take them up. Thus the
fungus, acts as a sink for nutrients (or reservoir) for further plant use.
The mechanism of uptake and release of nutrients especially is not well
known. The plant host supplies the fungus with reduced carbon
compounds such as the 6-C sugars (hexose). Then the fungus benefits
the plant in several ways such as:
a) The fungus increases the uptake of mineral nutrients and water

from the soil.
b) The fungus efficiently absorbs mineral nutrients that are in low
concentrations compared to non-mycorrhiza roots.
c) The fungal hyphae release hydrolytic enzymes that release N and
P from organic compounds. As a result of this mycorrhiza plants
are more competitive and better able to tolerate environmental
stresses than non- mycorrhiza plants.
3.3 Types of Mycorrhiza Fungi
Mycorrhiza fungi are regularly found in most soils and form extensive
network of hyphae that connect different plant species. It has been
observed and reported that on larger root systems, different fungi can
infect the same root system. Mycorrhiza fungi are classified based on
their structure and function namely:
a) Arbuscularmycorrhiza fungi (Endo-mycorrhiza)
b) Ecto-mycorrhiza
c) Ericaceous mycorrhiza (Ericord type)
d) Orchideceousmycorrhiza
e) Ectendomycorrhiza
The first two types are considered the most important especially in
agroecosystems and will be discussed in full in this unit.
45
SLM 505 MODULE 2
a) ArbuscularMycorrhizae (AM)
The most important in the group of endo-mycorrhiza association also
called endo-mycorrhiza or vesicular-arbuscularmycorrhiza. It is
preferably called Arbuscularmycorrhizae because not all form vesicles
but all have arbuscles. In this type of mycorrhiza, the fungus initially
grows between cortical cells, but soon penetrates the host cortical root
cell wall and grows within the cell. As the fungus grows, the plant cell
membrane invaginates and envelops the fungus, creating new structures
where materials of high molecular complexity are deposited. This
structure allows for efficient transfer of nutrients between the plant root
and the fungi. These structures are small and highly branched and called
arbuscules. They serve to transfer mineral nutrients from the fungi to
the host plant and sugar from the host plant to the fungus. Other
structures produced are residues, auxillary cells and asexual spores.
Vesicles are thin-wall, lipid filled structures which form in the
intercellular spaces and serve as storage organs and reproductive
propagules for the fungus. Auxillary cells are reported to form in soils
and their function is not known. Asexual spores (reproductive) are
formed either in the root or soil. The spores are asexual spores.
Examples of crop plants that form AM association are corn, cotton,
wheat, potatoes, soybean, sugarcane, cassava, rice, apples, grapes, citrus,
cocoa, coffee, rubber while cabbage, mustard, canola, broccoli, sugar-
beet spinach do not form AM association.
b) Ecto-mycorrhiza
They are associated with forest trees and shrubs like pine, birch, oak,
hemlock, spruce and fir found mostly in temperate or semiarid regions.
The fungi are mostly basidiomycetes. They grow between root cortical
cells producing net – like structure called Hartig net. They produce large
quantities of hyphae on the root and in the soil. Many of them produce
mushrooms on forest floor. These hyphalsheath (mantle) cover the
surface of absorbing root, thereby increasing the effective absorptive
surface area of the roots. The hyphae also absorp and translocate
inorganic nutrients and water. They also release nutrients from layers of
litter. The hyphae penetrate the roots and develop in the tree space
around the cells of the cortex but do not penetrate the cortex cell wall.
They form stubby white rootlets with a characteristic Y-shape (Hartig
net structure).
c) Ericaceous mycorrhizae
These are found on plants in the order Ericales (Ericaceous shrubs).
They dominate temperate soils that are high in organic matter (high
organic heathland soils). The ascomycetous fungi are among this group.
They grow within (intracellular) cortical cells (endomycorrhizal habit)
but with few or little extension into the soil. No arbuscules are formed.
The fungus produces extracellular enzymes that mineralize organic
46
matter (OM), thereby making the plants to have access to the nutrients
tied up in the OM.
d) Orchidaceous mycorrhizae
Found in the family Orchidaceae (orchids). Orchids have small seeds
with little nutrient reserve. The basidiomycetes are among this group.
The plant getscolonised after germination. The fungus supplies carbon
and vitamins to the developing embryo. The fungus grows into plant
cell, investigating the cell membrane forming hyphal coils within the
cell. The coils are active for a few days and then lose turgor (strength)
and degenerate, and the developing orchid absorbs the nutrient contents.
In the mature orchid, mycorrhizae enhance nutrient uptake and
translocation also.
e) Ectendomycorrhizae
This is a type of mixed mycorrhiza infection. It forms a typical
ectomycorrhizal structure, except that the mantle is thin or lacking and
hyphae in the Harting net may penetrate root cortical cells. As the
seedling matures, ecto-mycorrhiza is replaced by ectendomycorrhiza.
The fungi initially in this group are the designated “E-strain” and later
shown to be ascomycetes. In this type of mixed mycorrhiza infection,
the host can support more than one type of mycorrhiza association.
Examples of this type of mycorrhiza infection is found on Eucalyptus
tree (have both AM and Ectomycorrhizal association on the same
plant/tree).
Adapted from Brady and Weil (2002)
47
SLM 505 MODULE 2
3.4 Benefits of mycorrhiza fungi in ecosystems
The benefits of mycorrhiza fungi in the ecosystem are seen in its

functions and these are:
a) Increase effective absorptive root surface area. This is the root
parameter that controls uptake.
b) Increase nutrient uptake and transfer of immobile nutrients.
c) Mycorrhizae impact drought tolerance (improve water uptake)
d) Protect plant from uptake of excessive salt, heavy metal and Al in
saline, acid or contaminated soils.
e) Protect plant from pathogen association in the rhizosphere such
as parasitic nematodes, soil borne diseases by releasing
antibiotics, thereby altering root epidermis.
f) They (mycorrhizae) help in determining plant community
structure and plant succession.
g) They improve or help stabilise soil aggregate
h) Their presence enhance nodulation and N2 fixation by legumes.
3.5 Mechanism of nutrient uptake (especially P)
The fungi produce large quantities of hyphae on the root of plant and in
the soil. These hyphal mantle or sheath covers the surface of the
absorbing root, thereby increasing the effective absorptive surface area
of the absorbing roots. The mycorrhiza roots enhance the uptake of
mineral nutrients and water because the external mycelia explore greater
volume of soil. The fungus then absorbs mineral nutrients at low
concentrations more efficiently by producing various hydrolytic
enzymes that release N and P from organic compounds (OM) that are
unavailable to the plant.
What is mycorrhizae? and enumerate the types and functions of

mycorrhiza fungi in the soil environment.
3.6 Factors that Affect Mycorrhiza Fungi
a) Conventional agronomic practices affect adversely the diversity

and abundance of AM fungi e.g. soil tillage destroys the hyphal
networks and mono-cropping under long periods of fallow.
b) Application of large quantities of Phosphorus fertilisers inhibit
growth and activity of vegetative mycelium
c) When surface soil is stockpiled during mining and construction
activities, it loses its mycorrhiza inoculum potential.
d) Fumigant pesticides adversely affect AM activity in soil
e) Low light (photosynthate limiting) affect growth of mycorrhizae
48
f) Nutrient status of soil

g) Inoculum potential of the fungi.
4.0 CONCLUSION
From the discussion in this unit, mycorrhiza association is a symbiotic

interaction between a fungi and root of higher plant. Extensive network
of hyphae is produced that penetrate between or into the cortical cells
and soil. The plant supplies the fungus with reduced carbon while the
fungus benefits the plant by supplying the plant with nutrients and water
especially in deficient or infertile soil thereby improving plant growth
and reproduction. Hence, plants that have mycorrhiza association are
more competitive and able to withstand harsh environmental condition
than non-mycorrhiza plants. Mycorrhiza fungi are classified based on
their structure and function. Endo-mycorrhiza (AM) and ecto-
mycorrhiza are two important fungi in agroecosystem. The AM fungi
form highly branched structures called arbuscules which serve to
transfer mineral nutrients from fungus to the plant and sugars from plant
to the fungus. Other structures include vesicles (storage organs),
auxillary cells and asexual spores. Ectomycorrhizal fungi are mostly
basidiomycetes forming Hartig net. Several factors affect mycorrhiza
fungi such as host plant diversity and abundance, fertilizer application
(especially phosphate fertilizer), mining and construction activities,
pesticides and low light and the nutrient status of the soil. They improve
soil structure, nutrient availability and water uptake. They also give
protection to the plant against diseases and pathogen interaction in the
rhizosphere.
5.0 SUMMARY
From the discussion in this unit, a summary table is given below

indicating host plant, fungi and important functions of the mycorrhizal
associations
Mycorrhizal type Host involved Fungi involved Characteristic Characteristic

structures functions
Arbuscular Bryophytes Zygomycetes spp., Arbuscules Nutrient uptakes
Pteridophytes Glomeromycota vesicles soil aggregation
some Auxillary
gymnosperms cells
many
angiosperms
Ectomycorrhizae Mostly Basidiomycetes Hartig net Nutrient uptake,
gymnosperms, some ascomycetes Mantle mineralization of
some Few zygomycetes Rhizomorphs OM, soil
angiosperms aggregation
Restricted to
woody plants
Ericaceous Ericales Ascomycetes, Same with Mineralization of
49
SLM 505 MODULE 2
Basidiomycetes either Hyphae OM, transfer

in cell or between plants
Mantle and
net
Orchidaceous Orchidaceae Basidomycetes Hyphal coils Supply carbon
and vitamins to
embryo
Ectendomycorrhi Mostly Ascomycetes Hartig net, Nutrient uptake,
zae or mixed gymnosperms with some mineralization of
infection cell OM
penetrating,
Thin mantle
Adapted from Sylvia et al. (2007).
1) Discuss mycorrhiza association.

2) Explain their benefit in agroecosystem.
3) Identify mechanisms of nutrient uptake especially P.
4) Discuss the factors affecting mycorrhiza fungi.

(13thed.). Upper Saddle River, NJ:Prentice Hall.

(2nded.). New Jersey: Prentice Hall, Upper Saddle River,
50
SLM 505 MODULE 3
MODULE 3 MICROBIAL TRANSFORMATION OF

CYCLES IN SOIL
Unit 1 Soil Organic Matter Transformation

Unit 2 Nitrogen Transformation
Unit 3 Phosphorus Transformation
Unit 4 Sulphur Transformation
Unit 5 Iron Transformation
UNIT 1 SOIL ORGANIC MATTER

TRANSFORMATION
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Definition of Soil Organic Matter
3.2 Components of Soil Organic Matter
3.3 Importance of Soil Organic Matter
3.4 Microbial Processes in Organic Matter Transformation
3.5 Maintenance of Soil Organic Matter
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
The vast array of organic matter that is produced on earth during

photosynthetic processes does not keep accumulating, rather it is
consumed and degraded, and a delicate global balance of carbon is
maintained, CO2 is removed from the atmosphere during photosynthesis
and released during respiration. The balance is as a result of the
biologically driven, characteristic cycling of carbon, nitrogen,
phosphorus, sulphur and iron which are cycled in predictable and
definable ways between biotic forms and abiotic forms.
Understanding microbial transformation of cycles in soil allows scientist

to understand and predict the development of microbial communities
and activities in the environment. As decomposition of plant residues
proceeds, microbes slowly breakdown complex compounds into simpler
compounds. The soil microbes then metabolise the resulting simpler
compounds.
51
2.0 OBJECTIVES
• define soil organic matter

• explain the various components of soil organic matter
• discuss the importance of soil organic matter
• explain the role of microbes in organic matter transformation
• identify how soil organic matter can be maintained.
3.0 MAIN CONTENT
3.1 Definition of Soil Organic Matter
Soil organic matter consists of a wide range of organic substances,

including living organisms, remains of organisms that once occupied the
soil, and organic compounds produced by current and past metabolism
in the soil. The remains of plants, animals and microorganisms are
continuously broken down in the soil and new substance issynthesised
by other microorganisms.
3.2 Components of Soil Organic Matter
Classification of soil organic matter components is separable by

chemical and physical criteria. They include:
• Living organisms (Biomass).
• Identifiable dead tissue (Detrites).
• Non-living, non-tissue.
Humus
Humic substancesNon humic substances
Humic acid Fulvic acid
3.3 Importance of Soil Organic Matter
Soil organic matter is one of the best indications of good soil health
(nutrition and structure). There are two major roles or importance of soil
organic matter namely
• Improvement of physical properties of soil.
• Enhancement of microbial activitiesPhysical benefits.
• Reduces evaporation loss.
52
SLM 505 MODULE 3
• Stubble mulching.
• Surface mulches control soil erosion.
3.4 Microbial Processes in Organic Matter Transformation
As decomposition of plant residues proceeds, microbes slowly

breakdown complex compounds into simpler compounds
whilethe soil microbes then metabolise the resulting simpler
compounds.
Diverse populations of microorganisms are found in most productive

soils and total about several hundred million per gram. Thus, to maintain
organic matter, water and air are the critical factors that can limit
functions of microorganisms.
Microbial processes include:

• Organic matter decomposition
• Conversion of elements to plant available forms
• Nitrogen fixation.
Organic matter decomposition

A good rate of decomposition is required and the conditions that favour
rate of organic matter decomposition by microbes include:
• Adequate soil moisture
• Well aerated soil
• Adequate temperature (optimum)
• C:N ratio
• Quantity and quality of plant residue
• Size of plant materials.
Conversion of elements to plant available forms (e.g. nitrogen

transformation) changes in soil N and microbial activities are important
in farm management, For example,
• Ammonification – This is the process where organic nitrogen
compounds yield ammonia when they decompose or transform.
• Nitrification – The oxidation of ammonia to nitrate by action of
nitrifying bacteria Nitrosonomas bacteria oxidises ammonia to
nitrite while Nitrobacter bacteria oxidises nitrite to nitrate.
• Denitrification – This is the biological reduction of nitrate to
gaseous nitrogen. This is the most important way of loss of
available N in soils.
Nitrogen fixation
This is the process of conversion of atmospheric N into plant available
form by the action of microorganisms. Inoculation and growth of
53
leguminous plants has been major practical use of this, of recent the
discovery that N may be fixed by certain bacteria living in close
association with the roots of a number of tropical grasses has attracted
attention. Examples of N-fixing microorganisms are: Azotobacter,
Clostridium, Blue-green algae and Rhizobium.
3.5 Maintenance of Soil Organic Matter
The need to maintain organic matter in soil is of immense importance

for sustainable agricultural production. The maintenance or
improvement of organic matter includes:
• Crop or plant residues incorporation
• Use of green manures, mulching (cover crop)
• Farmyard or animal manure incorporation
• Compost application
• Use of urban and industrial wastes
• Rotation/Intercropping with legumes
• Fertiliser application and living
• Adoption of reduced tillage (minimum tillage).
4.0 CONCLUSION
In the unit, we have discussed the definition, components, importance,

and maintenance of soil organic matter as well as microbial processes in
organic matter transformation. Following these discussions, it can be
concluded that organic matter produced on earth does not keep
accumulating;ratherit is consumed and degraded by microbes for it to be
available for sustainable production as well as their importance
component and maintenance.
5.0 SUMMARY
In this unit we have learnt that:

• Soil organic matter consists of both living and dead remains of
plants and organisms as well as the substances they produce.
• Soil organic matter aids in improving soil structure, texture and
water holding capacity and how it can be maintained using some
materials.
• As decomposition of plant residues proceeds, microbes slowly
breakdown complex components into simpler compounds. And
soil microbes then metabolise the resulting simpler compounds.
• Understanding microbial transformation of cycles in soil allows
scientists to understand and predict the development of microbial
communities and activities in the environment.
54
SLM 505 MODULE 3
1) Define soil organic matter.

2) Explain the various components of soil organic matter.
3) Discuss the importance of soil organic matter.
4) Explain the role of microbes in organic matter transformation.
5) Identify how soil organic matter can be maintained.

(13thed.).Upper Saddle River:Prentice Hall.

(3rded.). Canada: Academic Press Publications.
Maier, R. M; Pepper, I. L &Gerba, C. P. (2009).Environmental

Microbiology.California: Academic Press, San Diego.

(2nded.)New Jersey: Prentice Hall, Upper Saddle River.
55
UNIT 2 NITROGEN TRANSFORMATION
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Nitrogen Cycle
3.2 Nitrogen Reservoirs
3.3 Importance
3.4 Transformations
3.4.1 Nitrogen Fixation
3.4.2 Ammonification
3.4.3 Nitrification
3.4.4 Denitrification
3.4.5 Immobilisation
3.4.6 Volatilisation
3.4.7 Mineralisation
3.4.8 Leaching
3.4.9 Crop uptake
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
More money and effort have been, and are being spent on the
management of nitrogen than any other mineral element. And for good
reason: The world’s ecosystems are probably influenced more by
deficiencies or excesses of nitrogen than by those of any other essential
element. Were it not for the biological fixation of nitrogen from the
atmosphere by certain micro-organisms, and for the recycling back to
the soil of much of the nitrogen taken up in natural ecosystems,
deficiencies of nitrogen would be even more widespread.
Nitrogen is an essential component of protein. Because of its nutritional

importance and relative scarcity, protein is highly sought after by most
animals, humans included. Supplying sufficient nitrogen often presents a
major expense in agricultural production.
The processes of the nitrogen cycle transform nitrogen from one form to
another. Many of those processes are carried out by microbes, either in
their effort to harvest energy or to accumulate nitrogen in a form needed
for their growth.
56
SLM 505 MODULE 3
2.0 Objectives
• understand the nitrogen cycle

• discuss its reservoirs
• discuss the importance of nitrogen
• explain the various transformations (interconnection and control.
3.0 MAIN CONTENT
3.1 Nitrogen cycle
There is great interest in the nitrogen cycle because nitrogen is the

mineral nutrient most in demand by micro-organisms and plants. It is the
fourth most common element found in cells, making up approximately
12% of cell dry weight. For example, nitrogen can exist in numerous
oxidation states, from -3 I ammonium (NH4+) to +5 in nitrate (NO3-).
The nitrogen cycle is the process by which nitrogen is converted
between its various chemical forms. This transformation can be carried
out through both biological and physical processes. Important processes
in the nitrogen cycle include fixation, ammonification, nitrification and
denitrification. The nitrogen cycle is dominated by microbial action.
3.2 Nitrogen Reservoirs

Nitrogen in the form of the inert gas, dinitrogen (N2), has accumulated
in earth’s atmosphere since the planet was formed. Nitrogen gas is
continually released into the atmosphere from volcanic and
hydrothermal eruptions, and is one of the major global resources of
nitrogen. A second major reservoir is the nitrogen that is found in earth’s
crust as bound, non-exchangeable ammonium. Neither of these
reservoirs is actively cycled; the nitrogen in earth’s crust is unavailable
and the N2 in the atmosphere must be fixed before it is available for
biological use. Because nitrogen fixation is energy – intensive process
and is carried out by a limited number of micro-organisms, it is a
relatively slow process. Smaller reservoirs of nitrogen include the
organic nitrogen found in living biomass and indeed organic matter and
soluble inorganic nitrogen salts.
3.3 Importance
Nitrogen is an integral component of many essential plant compounds. It
is a major part of all amino acids, which are the building blocks of all
proteins – including the enzymes, which control virtually all biological
57
processes. Nitrogen is also essential for carbohydrate use within plants.

A good supply of nitrogen stimulates root growth and development, as
well as the uptake of other nutrients. It can stimulate plant productivity
as well as increasing the plumpness of cereal grains, the protein content
of both seeds and foliage and the succulence of such crops as lettuce and
radishes.
3.4 Transformations
3.4.1 Nitrogen Fixation
Ultimately, all fixed forms of nitrogen, NH4+, NO3-, and organic N,
come from atmospheric N2. Nitrogen fixation is an energy – intensive
process and until recently was performed only by selected bacteria and
cyanobacteria. As fertilizers are expensive, management alternatives to
fertilizer addition have become attractive. These include rotation
between nitrogen-fixing crops such as soybeans and non-fixing crops
such as corn. Nitrogen is fixed into ammonia (NH3) by over 100
different free-living bacteria, both aerobic and anaerobic as well as some
Actinomycetes and cyanobacteria. For example, Azotobacter (aerobic),
Beijerinckia (aerobic), Azospirillium (facultative), and Clostridium
(anaerobic) can all fix N2. Because fixed nitrogen is required by all
biological organisms, nitrogen fixing organisms occur in most
environmental niches Symbiotic nitrogen fixing bacteria such as
Rhizobium usually live in the root nodules of legumes (such as peas,
alfalfa and locust trees).
3.4.2 Ammonification
The release of ammonium from organic nitrogen compounds by broad
groups of heterotrophic organism is called ammonification
Organic N NH4+
3.4.3 Nitrification
The conversion of ammonia to nitrate is performed primarily by soil
living bacteria and other nitrifying bacteria. In the primary stage of
nitrification, the oxidation of ammonium (NH4+) is performed by
bacteria such as the Nitrosomonas species, which converts ammonia to
nitrites (NO2-). Other bacterial species such as Nitrobacter, are
responsible for the oxidation of the nitrites into nitrates (NO3-). It is
important for the ammonia to be converted to nitrates or nitrites because
ammonia gas is toxic to plants.
3.4.4 Denitrification
58
SLM 505 MODULE 3
Denitrification is the reduction of nitrates back into the largely inert

nitrogen gas (N2), completing the nitrogen cycle. This process is
performed by bacterial species such as pseudomonas and clostridium in
anaerobic conditions. They use the nitrate as an electron acceptor in the
place of oxygen during respiration these facultative anaerobic bacteria
can also live in aerobic conditions. Denitrification happens in anaerobic
conditions e.g. waterlogged soils. The denitrifying bacteria use nitrates
in the soil to carryout respiration and consequently produce nitrogen gas,
which is inert and unavailable to plants.
This is the reverse of mineralisation. All living things require N,
therefore microorganisms in the soil compete with crops for N.
Immobilisation refers to the process in which nitrate and ammonium are
taken up by soil organisms and therefore become unavailable to crops.
Incorporation of materials with a high carbon to nitrogen ratio (e.g. saw
dust) will increase biological activity and cause a greater demand for N
and thus result in N immobilisation.
3.4.6 Volatilisation
It is the loss of N through the conversion of ammonium to ammonia gas,
which is released to the atmosphere. The volatilisation losses increase at
higher soil pH and conditions that favor evaporation (e.g. hot and
windy).
It is the process by which microbes decompose organic N from manure,
organic matter and crop residues to ammonium. Because it is a
biological process, rates of mineralisation vary with soil temperature,
moisture and the amount of oxygen in the soil (aeration).
3.4.8 Leaching
It is the pathway of N loss of a high concern to water quality. Soil
particle do not retain nitrate very well because both are negatively
charged. As a result, nitrate easily moves with water in the soil. The rate
of leaching depends on soil drainage, rainfall, amount of nitrate present
in the soil and crop uptake.
3.4.9 Crop uptake

This is the prime goal of N management on farms. The greatest
efficiency occurs when adequate N is applied at a time when the crop is
actively taking it up.
59
4.0 CONCLUSION
In this unit, we have discussed the nitrogen cycle, nitrogen reservoirs,
importance and the various transformations how they are interconnected
and controlled. Following these discussions, it can be concluded that
nitrogen is essential for agricultural production, the processes of the
nitrogen cycle transform nitrogen from one form to another and these
processes are carried out by microbes.
5.0 SUMMARY
• Nitrogen in an essential nutrient that is in demand by
microorganisms and plants.
• Nitrogen is gotten from different reservoirs.
• All the transformation processes in nitrogen are interconnected
and controlled.

1) Explain the nitrogen cycle.
2) Discuss its reservoirs.
3) Discuss the importance of nitrogen.
4) Explain the various transformations (interconnection and control.

Alexander, M. (1991).Introduction to Soil Microbiology. (2nded.).Wiley,
New York.

(13th ed.), Upper Saddle River, NJ: Prentice Hall,

(3rded.) .Canada: Academic Press Publications,

Microbiology.San Diego, California: Academic Press,.
Soil Science Society of America (1997).Glossary of Soil Science

Terms.SSSA, madison, WI.138pp. Available online at
www.soils.org/sssagloss/.
60
SLM 505 MODULE 3

(2005).Principles and Applications of Soil Microbiology.(2nded.).
New Jersey: Prentice Hall, Upper Saddle River,.
61
UNIT 3 PHOSPHORUS TRANSFORMATION
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Phosphorus Cycle
3.2 Phosphorus Reservoirs
3.3 Importance
3.4 Transformations
3.4.3 Oxidation and Reduction
3.4.4 Solubilisation
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Soil microorganisms have a profound effect on the transformations

involved in a large number of biogeochemical cycles other than C and
N, such as the macronutrients phosphorus (P) and sulphur (S), and
various micronutrients and environmental pollutants.
Phosphorus is found in soil, plats and in microorganisms in a number of

organic and inorganic compounds. It is second only to nitrogen as
mineral nutrient required by plants and microorganisms, its major
physiological role being in certain essential steps in the accumulation
and release of energy during cellular metabolism.
2.0 OBJECTIVES
• explain the phosphorus cycle

• explain the importance of phosphorus
• discuss the various microbial transformations.
62
SLM 505 MODULE 3
3.0 MAIN CONTENT
3.1 Phosphorus Cycle
Phosphorus cycle is similar to several other mineral nutrient cycles in

that P exist in soils and minerals, living organisms and water. Although
P is widely distributed in nature, P is not found by itself in elemental
form. The phosphorus cycle is the process by which phosphorus is
converted between its chemical forms. Important processes in the
phosphorus cycle include mineralisation, immobilisation, oxidation and
reduction and solubilisation.
3.2 Phosphorus Reservoirs
The largest global reservoir of P is the ocean sediment pool which

represents a small but steady sink for terrestrial P released by the
weathering of minerals or released by the biota. Phosphorus occurs
mainly in inorganic phosphates and in organic phosphates derivatives.
Phosphorus in organic molecules constitutes 30 – 50% of the total P in
most soils, ranging from as low as low as 5% to as high as 95%.
3.3 Importance
Phosphorus is an element essential to life. It plays both structural and

functional roles in virtually all organisms and is found in cell
components such as phospholipids, nucleic acids, and DNA as well as
promoting root growth and stimulatestillering and hastens maturity
which isimportant in cell division and development of new tissues.
3.4 Transformations
Organically bound P is not directly available to organisms because it

cannot be absorbed into cells in this form. For cellular uptake to occur, P
must first be released from the organic molecule through the action of
phosphate.
Soil microorganisms can cause fixation or immobilisation of P, either by

promoting the formation of inorganic precipitates or by assimilation into
organic cell constituents or intracellular polyphosphate granules. The
63
extent of immobilisation of P as affected by the C:P ratio of the organic

materials being decomposed and the amount of available P in solution.
A number of soil bacteria and fungi have been shown to be capable of

oxidising reduced phosphorus compounds (e.g. phosphite) either
aerobically or anaerobically. The biochemical pathway for such a
microbially medicated reaction has been characterised molecularly and
generally, providing some evidence for a previously under-appreciated
microbial redox cycle for P.
3.4.4 Solubilisation
The low solubility of P in soils makes it one of the major nutrients

limiting plant growth. Frequent applications of soluble forms of P are
needed, more than really necessary, because only a fraction is used by
plants while the rest rapidly forms insoluble complexes. Traditional P
fertilizer production is based on chemical processing of insoluble
mineral phosphate ore, which is expensive and environmentally
undesirable. In areas where commercially produced P fertilizer is to
costly, the microbial solubilisation of phosphate rock is seen as a viable
alternative.
4.0 CONCLUSION
In this unit, we have discussed the phosphorus cycle, phosphorus

reservoirs, importance and the various transformations how they are
interconnected and controlled. Following these discussions, it can be
concluded that phosphorus is essential for agricultural production, the
processes of the phosphorus cycle transform phosphorus from one form
to another and these processes are carried out by microbes.
5.0 SUMMARY

• Phosphorus is an essential nutrient most in need by
microorganisms and plants.
• Phosphorus is found in soil, plant and in microorganisms in a
number of organic and inorganic compounds.
• Important processes in the phosphorus cycle include
mineralisation, immobilization, oxidation and reduction and
solubilisation.
1) Explain the phosphorus cycle.

64
SLM 505 MODULE 3

3) Explain the importance of phosphorus.
4) Discuss the various microbial transformations.

(13th ed.), Upper Saddle River, NJ: Prentice Hall,

(3rded.). .Canada: Academic Press Publications,

Microbiology.California: Academic Press, San Diego,.

Terms.SSSA, Madison, WI.138pp.Available Online at

(2005).Principles and Applications of Soil Microbiology. (2nded.).
New Jersey: Prentice Hall, Upper Saddle River.
65
UNIT 4 SULPHUR TRANSFORMATION
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 SulphurCycle
3.2 SulphurReservoir
3.3 Importance
3.4 Transformations
3.4.3 Oxidation
3.4.4 Reduction
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Soil microorganisms have a profound effect on the transformations

involved in a large number of biogeochemical cycles other than C and
N, such as the macronutrients phosphorus (P) and sulphur (S), and
various micronutrients and environmental pollutants.
Sulphur is a mineral nutrient required by plants and microorganisms, its

major physiological role being in certain essential steps in acids
stabilisation of protein structure, metabolic activities of vitamins, biotin,
thiamine and coenzymes A.
2.0 OBJECTIVES
• discuss the sulphur cycle

• explain its reservoirs
• explain the importance of sulphur
• discuss the various microbial transformation.
66
SLM 505 MODULE 3
3.0 MAIN CONTENT
3.1 SulphurCycle
The terrestrial sulphur cycle involves significant interactions between

the pedosphere, the hydrosphere the biosphere, and the atmosphere. The
S cycle is similar to the soil N cycle and unlike P, these elements
undergo chemical and microbial mediated transformations leading to
volatilization. Not only is the biosphere a repository for highly mobile
forms of S, but several key reactions of the cycle are accelerated by, and
sometimes completely controlled by microbiological activity.
3.2 SulphurReservoir
The largest global reservoir of S is the lithosphere. The atmospheric

content of S represents a relatively small pool, but one that has increased
significantly in recent times due to the burning of fossil fuels.
3.3 Importance
Sulphur is an element essential to life. It serves as a building block of

proteins and vitamins, key ingredient in chlorophyll formation, synthesis
of oils, increases crop yield and improves quality and the activation of
enzymes.
3.4 Transformations
Carbon-bonded S is mineralised through various pathways:

• Direct aerobic mineralisation during the oxidation of C as an
energy source
• Anaerobic mineralisation of organic matter (desulfurisation)
• Incomplete oxidation of organic S into inorganic S compounds
• Biological oxidation of H2S to sulphate via element S and
sulphite.
Inorganic S is usually assimilated into organic compounds as SO42- by

plants and most microorganisms.
67
3.4.3 Oxidation
In the presence of available election acceptors, reduced forms of S are

oxidized by both chemical and microbial pathways: A wide variety of
organisms are capable of oxidising S in a wide variety of environments.
e.g. green and purple sulphur bacteria, Bacteria, Fungi, Arthrobacter,
Bacillus and Pseudomonas, etc.
3.4.4 Reduction
Reduction of oxidized forms of S, particularly SO42-, by micro-

organisms occurs in two different ways. I the first, S is incorporated into
cellular constituents such as the S in amino acids. This process is
referred to as assimilatory sulphate reduction, or immobilization as
described above. In the other, the reduction leads to the following of
sulphide (e.g. H2S) as the end product.
This is referred to as dissimilatory, or respiratory, sulfate reduction. This

process is mediated by anaerobic, oligotrophic organisms that use low-
molecular weight organic compounds or H2 as electron donors and the
oxidised S compounds as terminal electron acceptors in a process
similar to denitrification.
4.0 CONCLUSION
In this unit, we have discussed the sulphur cycle, phosphorus reservoirs,

importance and the various microbial transformations. Following these,
it can be safely concluded that sulphur is an essential element to life and
agricultural productivity, the processes of the sulphur cycle transform
sulphur from one form to another and these processes are carried out by
microbes.
5.0 SUMMARY
• Sulphur is an essential element to life

• It largest reservoir is the lithosphere
• Important processes in the sulphur cycle include mineralisation,
immobilisation, oxidation and reduction.
1) Discuss the sulphur cycle.

2) Explain its reservoirs.
68
SLM 505 MODULE 3
3) Explain the importance of sulphur.

4) Discuss the various microbial transformation.
Brady, N.C. &Weil, R.R. (2002).The nature and properties of soils.13th

edition, Prentice Hall, Upper Saddle River, NJ. 881pp.


Microbiology.San Diego, California: Academic Press.

Terms.SSSA, Madison, WI.138pp. Available Online at

(2nded.). , New Jersey: Prentice Hall, Upper Saddle River.
69
UNIT 5 IRON TRANSFORMATION
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Iron
3.2 Iron Reservoir
3.3 Importance
3.4 Transformation
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Despite the fact that it is only a minor nutrient for the growth of most of
the microscopic life of the soil, iron is an element which readily
undergoes transformation through the activity of the microflora. Iron is
always abundant in terrestrial habitats, and it is one of the major
constituents of the earth’s crust. Microorganisms are implicated in the
transformations of iron in a number of distinctly different ways, and the
form of the element may be affected through a variety of biological
means.
2.0 OBJECTIVES
At the end of the unit, you should be able to:
• identify iron cycling in soil

• explain the microbial transformations.
3.0 MAIN CONTENT
3.1 Iron
3.2 Iron Reservoir
Iron is the fourth most abundant element in earth’s crust. Iron generally
exists in three oxidation states: 0, +2 and +3 corresponding to metallic
70
SLM 505 MODULE 3
iron (Feo), ferrous iron (Fe2+) and ferric iron (Fe3+). In the environment,
iron is actively cycled between the +2 and +3 forms. Under aerobic
conditions iron is usually found in its most oxidised form (Fe3+) which
has low aqueous solubility. Under reducing or anaerobic conditions Fe3+
is reduced to the ferrous form, Fe2+, which has higher solubility. Iron is
an essential but minor element for biological organisms, making up
approximately 0.2%of the dry weight of a bacterial cell.
3.3 Importance
Iron is an essential component of many enzymes, necessary for the

synthesis and maintenance of chlorophyll in plants, and plays an
essential role in nucleic acid metabolism.
3.4 Transformation
Biologically mediated, reduction-oxidation reactions are often

associated with energy production by the organisms. Reduced inorganic
compounds are oxidized by chemoautotrophs to generate electrons used
in ATP production, while oxidized compounds are reduced as an
alternative terminal electron acceptor. Micro-organisms are involved in
the oxidation of Fe, but not all Fe oxidation is microbial mediated.
Ferrous iron (Fe2+) is rapidly oxidized chemically in aerated solution at
pH 5. It is therefore difficult to demonstrate conclusively the microbial
role of Fe oxidation under mental or alkaline pH conditions. The best
evidence for microbial mediated Fe oxidation is from acidophilic
bacteria operating at pH 5.
4.0 CONCLUSION
In this unit, we have discussed iron and its reservoir, importance and its
microbial transformation. Following these, it can be concluded that iron
though a minor nutrient but essential. The process of its transformation
from one form to another is carried out by micro-organisms.
5.0 SUMMARY

• Iron is a minor nutrient but essential
• Iron is always abundant in terrestrial habitats
• Important process in iron cycle is oxidation and reduction
71
1) Identify iron cycling in soil.

3) Explain the microbial transformations.

(13thed.), Upper Saddle River, NJ: Prentice Hall,

(3rded.).Canada: Academic Press Publications..

Microbiology.San Diego, California: Academic Press..
Soil Science Society of America (1997).Glossary of Soil

Scienceterms.SSSA, Madison, WI.138pp.Available online at

(2005).Principles and Applications of Soil Microbiology. (2nded.).
New Jersey: Prentice Hall, Upper Saddle River,
72
MODULE 4
UNIT 1 WHAT ARE ENZYMES?
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 The Definition of Enzymes
3.2 Soil Enzymes
3.3 Properties of Enzymes
3.4 Role of Soil Enzyme Activities
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Enzymes are biological catalyst that helps to speed up the rate of

reactions without themselves being affected in the reaction or without a
permanent change. Most reactions in biological systems take place with
the aid of enzymes. The need to study enzymes therefore becomes
important considering the fact that these enzymes are involved in almost
all biological reactions. The study of these reactions in most proper and
convenient way will not be possible if it is not incorporated with the
study of enzymes, hence the term enzymology.
2.0 OBJECTIVES
• describe soil enzymes

• explain the properties of enzymes
• discuss the roles of soil enzyme activities
3.0 MAIN CONTENT
3.1 The definition of enzymes
Enzymes are biological catalysts that help speed up the rate of a reaction
without undergoing any permanent change or alteration. They are
specialised proteins that combine with a specific substrate and act to
72
SLM 505 MODULE 4
catalyse a biochemical reaction (specific activators). That is, they are

specific for the types of chemical reactions they participate in.
The rate of reaction is the amount in moles or grams of reacting particles

transformed or products formed per unit time.
3.2 Soil Enzymes
Soil is a living system where all biochemical activities proceed through

enzymatic processes. Sources of enzymes in soil are primarily the
microbial biomass, though they can also come from plant and animal
residues.
Enzymes accumulated in soils are present as free enzymes such as exo-

enzymes (extra-cellulars release from living cells); endo-enzymes (intra-
cellar released from disintegrating cells; and enzymes bound to cell
constituents (enzymes present in disintegrating cells, in cell fragments,
and in viable but non proliferating cells)
Free enzymes in soils are adsorbed on organic or mineral constituents or

complexed with humic substances or both. The amount of free enzymes
in the soil solution is small compared to that in the adsorbed state. Most
of the enzymes added to soil by decaying microbial tissues and plant and
animal residues are degraded by soil protease and what remains is
incorporated with humus.
Therefore, soil as a system of humus and minerals contain both

immobilised enzymes and occluded microbial cells. Each of the organic
and mineral fractions in soil has a special effect on enzyme activity.
3.3 Properties of Enzymes
1) The catalytic activity of most enzymes requires the activity of

some components called cofactors.Cofactors are organic or
inorganic components require for enzyme activity. A cofactor can
be inorganic (metal ions like Fe2+, Mg2+, Mn+) or organic like
cytochromes. When cofactors are covalently bound to an enzyme,
they are called Coenzymes. It is therefore, important to note that
the catalytic of an enzyme is inefficient without cofactors. The
protein component of an enzyme called Apo-protein.Apo-protein
complexes with cofactors to form an active enzyme able of
catalytic activity are called Holoenzyme (Aproprotein +
cofactor).
73
2) Most enzymes are proteins contrary to the former opinion about

enzymes that all enzymes are proteins. It has been observed that
some nucleic acids (RNA molecules) have catalytic activity.
3) Enzymes are specific. They are specific in both choice of

substrate and the reaction they catalyse. e.g. (1) proteolytic
enzymes act on proteins and never on lipids. (2) Trypsin is
specific for clearing the carboxyl bond (-Co-) of Arginine and
lysine on a polypeptide chain.
Also, specificity of enzymes can either be group specificityor

stereo-specificity. In group specified, the enzyme is specific for
group of substrates. E.g. Amino acid oxidase – act as an oxidase
enzyme in any amino acid. In stereo-specificity, the enzyme is
specific for a particular stereo-isomer e.g. Arginine will only act
on L-Arginine and not D – Arginine.
4) E+S ES E+P
Enzyme active site
Enzymes (E) have the capacity to form ES (enzyme substrate

complex) during catalytic activity. The association of the E and S
in the ES complex during catalytic activity is through the region
or portion of the enzyme called the Active Site (AS). The AS of
an enzyme is the region that binds the S and contributes the
residues that are involved in catalytic activities (breakage or
formation of bonds). These residues are called catalytic groups.
5) Enzymes have high turnover number (TON) compared to

conventional catalyst.
TON= Number of moles of product per minute or per second
produced by 1 mole of an active enzyme in a condition whereby
the enzyme is saturated with the substrate.
6) Enzymes (Es) catalyse reactions by lowering the activation

energy (Ea) of that particular reaction
7) Enzymes catalyse reactions without changing the equilibrium

constant of the reaction.
K1
e.g. A + B C+D
K2
[C ][ D] K
Keg = = keg 2
[ A][ B] K1
V1 = K1[A][B], V1 = 20 sec-1
V2 = K2[C][D], V2 = 40 sec-1
74
SLM 505 MODULE 4
keg = 2
Some enzyme reactions can be regulated. The regulation of enzyme

activity can be in various forms:
a) Covalent modification:Some enzymes are regulated by covalent

groups or addition of certain group or modification of enzymes
with a group. E.g.the enzyme that breaks down glycogen. This
enzyme is converted to an active form by addition of a PO4-
(phosphate) group.
b) Feedback inhibition: This mode of enzyme regulation is typical

for reactions that involve steps, e.g. formation of isoleucine from
Threomine – the reaction has about four different steps namely:
Th B – C – D – Isoleusine (Ile)
Inhibition process
Reaction of Threominedeaminase
byIsoleusine
1. Catalysis by threominedeaminase
2. Inhibition by high concentrations of product Isoleucine thereby
stopping the chain reaction
3. Conversion of inactive forms of enzymes (Zymogens) to active
forms
4. Cleavage of certain bond or groups in enzymes e.g. (2)
Typsinogen is the inactive form of enzyme trypsin (active form).
Trypsin formed by cleavage of certain peptide bonds.
3.4 Role of Soil Enzyme Activities
1) Soil enzyme activities are indicators of soil quality because they

play important role in soil biology and respond rapidly to changes
in soil management.
2) Soil enzyme activities respond to agronomic practices like
fertilizer, amendments, vegetation cover, pesticides and soil
conversation practices.
3) They are important components of soil humus and take part in
biochemical fertility of the soil.
75
4) Because all biochemical transformations in soil are dependent on

or related to the presence of enzymes, therefore soil enzyme
activities gives an insight into the biochemical processes in soil.
5) Soil enzyme activities are substrate specific and are related to
specific reactions.
i) Differentiate between cofactors, prosthetic group and coenzymes.

ii) Differentiate between Apo-protein and holoenzyme.
iii) Differentiate between covalent modification and feedback
inhibition.
4.0 CONCLUSION
From this unit, it can be concluded that:

• Enzymes are biologically specialised proteins and combine with
specific substrate to catalyse all biochemical reactions without
undergoing permanent alteration.
• Their catalytic activity requires the activity of some components
of the enzymes.
• The primary source of soil enzymes is microbial biomass and is
free living soil as either endo- or exo-enzymes.
• They respond rapidly to changes in soil management hence are
used as indicators of soil quality.
5.0 SUMMARY
From the discussions in this unit, it can be summarized that soil

enzymes are biologically specialized protein that are specific in their
reactions and their activities requires the activity of some components of
the enzyme. They are of great importance in soil quality assessment due
to their rapid response to changes in soil management. Hence, the need
to select indicators such as soil enzymes which show adverse effects on
yields become serious
1) Describe soil enzymes.

2) Explain the properties of enzymes.
3) Discuss the roles of soil enzyme activities.
76
SLM 505 MODULE 4


Publishing Agency
Nelson, D.L. & Cox, M.M. (2002).Lehninger Principles of

Biochemistry.(3rded.). .New York: India New Delhi for Worth
Publishers.
.
Palmer, T. (2001).Enzymes: Biochemistry, Biotechnology and Chemical
Chemistry. 3rded.). Chichester, England: Horwood Publishing,.
Price, N.C. & Stevens, L. (1999).Fundamentals of Emzymology.

(3rded.).Oxford: Oxford University Press.
77
UNIT 2 ENZYME CLASSIFICATION AND

NOMENCLATURE
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Classes of Enzyme
3.1.1 Class 1 – Oxidoreductases
3.1.2 Class 2 – Transferases
3.1.3 Class 3 – Hydrolases
3.1.4 Class 4 – Lyases
3.1.5 Class 5 – Isomerases
3.1.6 Class 6 – Ligases
3.2 Enzyme Nomenclature
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Enzyme nomenclature and classification came to be as a result of the

realization that different enzymes have similar names and the same
enzymes discovered by different scientists were having different needs.
In 1995, the IUPAC and IUB came together to set up an enzyme
commission (EC) which is responsible for:
• Development of a standard way of enzyme classification

• Development of a standard way of enzyme nomenclature
• Development of a standard unit of enzyme activity
• Development of standard methods of enzyme assay
In 1961, the EC submitted its first report. Based on the report, enzymes
where classified into six (6) different classes.
2.0 OBJECTIVES
• write the trivial and systematic names of enzymes

• give the figurative representation of enzymes
• explain or differentiate between the various classes of enzymes
78
SLM 505 MODULE 4
3.0 MAIN CONTENT
3.1 Classes of Enzymes
3.1.1 Class 1 – Oxidoreductases
This group of enzymes catalyses oxidation-reduction reactions. In most

reactions involving oxidoreductase NADH, NADPH, NAD+ and NADP+
serve as donors and acceptors respectively. In most cases NADH and
NAD+ serve the same purpose. These enzymes are further subdivided
into six or more different sub-classes such as:
1) Dehydrogenases
These enzymes catalyse dehydrogenation reactions, e.g. Alcohol
dehydrogenase
NAD+
Ethanol aldehyde + NADH + H+
alcoholdehydrogenase
2) Oxidases
These are enzymes that catalyse addition of oxygen into a
substrate with the resultant formation of hydrogen perioxide
(H2O2). In some oxidase enzyme reactions, water molecules are
formed instead of H2O2.
e.g. cytochromeoxidase
Glucose gluconolactone + H2O2

Glucose oxidase
3) Oxygenases
These enzymes catalyse the addition of molecular oxygen (O2)
into a substrate
e.g. catechol oxidase
O2
Catechol Cis-muconica
Catechol oxidase
4) Hydroxylases
These enzymes catalyse addition of O2 into a substrate with
resultant formation of a molecule of water (H2O).
NADP+ + H+ + O2
e.g. progesterone + deoxycorticosterone
79
hydroxylase
5) Peroxidases
These enzymes use H2O2 as anoxidant
H2O2 + NADH + H+ 2H2O + NAD+
6) Catalyses
In these enzymes H2O2 serve as an electron donor and electron
acceptor and helps in regulating the H2O2 produced in living
cells.
e.g.
H2 O2 + H 2 O 2H2O + O2
catalase
3.1.2 Class 2 – Transferases
These enzymes catalyse the transfer of groups and/or subgroups from a

donor to an acceptor. The subclasses include:
1) Kinases (enzymes transferring phosphate groups)
2) Transaminases (enzymes transferring NH2 group)
3) Glycosyltransferases (enzymes transferring
glycosyl groups)
Other transferases are involved in the transfer of one methyl group (1-
carbon transfer), ethyl group among others.
3.1.3 Class 3 – Hydrolases
These enzymes catalyse the hydrolytic cleavage of a group from the

molecule. The bonds undergoing the cleavage include C-N, C-C, C-S
and C-O bonds. The subclasses include peptidases, esterases,
phosphatases, β-glucosidasesulphatases among others.
3.1.4 Class 4 – Lyases
These enzymes catalyse the removal of groups or subgroups with the

introduction of a double bond. The subclasses include decarboxylases,
citratelyases, deaminase.
3.1.5 Class 5 – Isomerase
These are groups of enzymes that catalyseisomerisation reaction which

includes cis-trans isomeriosm, keto isomerism, epimerism among others.
Isomerases can act as mutases (enzymes that catalyse the intramolecular
arrangement of groups) or as Racemase (enzymes that catalyse the
conversion of L-stereoismer to a D-stereoisomer. Also Epimerase is
another subclass which catalyseepimerisation reactions.
80
SLM 505 MODULE 4
3.1.6 Class 6 – Ligases
These are group of enzymes that catalyse the addition of two groups at
the expense of ATP – Adenosinetriphosphate (ATP is hydrolysed during
the reaction) or another form of triphosphate. Ligases can also be called
synthetases.
3.2 Enzyme Nomenclature
In the nomenclature of enzymes, two important parameters are to be

noted. First, the systematic name and secondary the figurative
representation or classification of the enzyme. It is important to note that
apart from trivial names of enzymes, systematic names also exist. In the
figurative representation/classification, four figures are involved. The
first (1st) figure denotes the class of enzyme and the last figure denotes
the number of the enzyme in the list of enzymes belonging to the group.
The 2nd and3rdfigures depends on the class of enzymes and may differ
with respect to classes of enzymes.
a) Oxidoreductases
In naming this class of enzymes, the 2nd digit denotes the group involved
in oxidation-reduction (donor) and the 3rd digit denotes the acceptor
molecule. The table below shows the figurative representation of
oxidoreductase class of enzymes.
2nd digit (donor, group involved in 3rd digit (acceptor

oxidation – reduction) molecule)
1 Alcohol Primary (1o and 1 NAD+, NADP+
o
secondary 2 )
2 Aldehyde 2 Cytochrome, Fe3+
3 C2H5 (-C-C-) 3 O2 (oxygen)
4 1o amine
5 2o amine
6 NADH
e.g. Alcohol dehydrogenase EC 1.1.1.1
b) Transferases
2nd digit (group transferred) 3rd digit (chemical nature of the

group transferred)
1 One carbon atom 1 Methyl group
2 Aldehyde or ketone 2 Hydroxymethyl group
3 Acyl 3 Acids (carboxyl)
81
4 Glycosidic (carbohydrate)
5 Alkyl group (except methyl
(-CH3 group)
6 Nitrogenous group
7 Phosphate(phosphorus
containing group)
8 Sulphate group
e.g. Glucokinase EC 2.7.1.2
c) Hydrolases
The trivial names for enzymes under this class are mostly in the form of
addition of “ases” at the end of the substrate undergoing hydrolytic
action e.g. in glycosidase, the glycosidic bond is cleaved hydrolytically.
In the systematic name for hydrolase enzymes, the word hydrolase is
written after the substrate being hydrolysed. The 2nd and 3rd digits
denotes type of bond being hydrolysed and specific nature of the
chemical groups hydrolysed respectively as shown below:
2nd digit (bond type hydrolysed) 3rd digit (chemical nature of
the group hydrolysed)
1 Esther 1 Acid C-O-
2 Glycosidic 2 Thiolesther C-S-
3 Ether 3 Phosphate monoesther
O- -P=O
4 Peptide 4 Phosphate diester

5 C-N O-P-P=O
6 Acid anhydride
7 C-C
8 Acid halide
P-N
e.g. Acid phosphate EC 3.1.3.2
d) Lyases
The systematic name involves the addition of “Lyase’ after the substrate
undergoing the enzyme reaction. The trivalnames involves
decarboxylase indicating elimination of CO2 (carbondioxide). Example
of a typical trival name is Oxaloacetate decarboxylase. The enzyme
decarboxylates oxaloacetates. The systematic name should be
oxaloacetate carboxylase (EC 4.1.1.3).
2nd digit (type of bond lysed) 3rd digit (chemical nature of

the group lysed)
1 C-C 1 Carboxylic acids
2 C-O 2 Aldehydes
82
SLM 505 MODULE 4
3 C-N 3 Keto acids

4 C-S
e.g. Oxolocarboxyacetate EC 4.1.1.3
e) Isomerases
Here, the name of the substrate undergoing isomerisation reaction is
written first followed by the type of isomerism. E.g. Glucose-6-
phosphate-1-epimerase (G-6-P-1 epimerase) EC 5.1.3.1
2nd digit (type of isomerisation) 3rd digit (nature of the group

isomerisation)
1 Isomerism at a chiral centre 1 Amino acids
(e.g. Racemase, epimerism)
2 Cis-trans isomerism 2 Hydroxyacids
3 Intramolecular 3 Carbohydrates
oxidation/reduction
4 Intramolecular group transfer
f) Ligases
In the nomenclature of ligase enzyme the systematic name is written as
two groups undergoing ligation
e.g. A + B A – B 1st group =:
A:B ligase 2nd group = ligase
The trivial name of ligase enzyme is synthetase. All synthetase reactions

utilize energy from ATP. E.g. (1) Acetyl CoA synthetase (Trivial name)
Acetate: COASH ligase (systematic name)
EC 6.2.1.1
2nd digit (type of bond formed) 3rd digit (nature of chemical

bond formed)
1 C-O 1 Amide bond –C-NH2
2 C-S 2 Peptide bond –C-N-
3 C-N (mostly considered in 3rd 3
digit)
4 C-C
5 O-P
e.g. (2) Glutamine synthetase (Trival name) L-glutamate:ammonia

ligase (systematic name)
EC 6.3.1.2
83
i. Write the trivial and systematic names of two enzymes from each
class of enzyme and give the figurative representation of each.
ii. Write noting their 4th digits/figures.
4.0 CONCLUSION
From the unit, it can be concluded that enzymes are classified into six
classes and each class has subclasses, using the standard developed by
enzyme commission (EC). The systematic name and figurative
representation or classification is the two important parameters in
enzyme nomenclature. Four figures or digits are involved in the
figurative representation.
The 1st being the class of enzyme while the last denotes the number of
the enzyme in the list of enzymes in that group. The 2nd and the 3rd digits
figures depends on the class of enzyme and differ due to their classes.
5.0 SUMMARY
Having realised that different enzymes have similar names and different
needs, it became necessary to set up an enzyme commission that
developed the standard for enzyme classification and nomenclature
putting into consideration enzyme activities and enzyme assays.
Enzymes were classified into six classes as shown below:
Class Catalytic function

1 Oxidoreductases Oxidation – reduction reaction
2 Transferases Group transfer reaction
3 Hydrolases Hydrolysis reactions (i.e. hydrolytic
cleavage reactions)
4 Lyases Reactions involving removal of a group
(leaving a double bond) or addition of a
group to a double bond
5 Isomerases Reactions involving isomerisations
6 Ligases Reactions joining together two molecules
coupled with the utilisation of high energy
bonds
1) Write the trivial and systematic names of enzymes.

2) Give the figurative representation of enzymes.
3) Explain or differentiate between the various classes of
enzymes.
84
SLM 505 MODULE 4
Eldor, A.P. (Ed.) (2007). Soil Microbiology, Ecology and

Biochemistry.(3rded.). Canada:.Academic Press Publications,
Nelson, D.L. &Cox, M.M. (2002).Lehninger Principles of

Biochemistry.(3rded.)..New York.:India, New Delhi, Worth
Publishers.

Chemistry. (3rded.). Chichester, England: Horwood Publishing,.
Price, N.C. &Stevens, L. (1999).Fundamentals of Enzymology.

(3rded.).Oxford: Oxford University Press,.

Terms.SSSA, Madison, WI.138pp.Available online at
85
UNIT 3 SOIL ENZYMES IMPORTANT IN

AGRICULTURE
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Soil Enzymes Important in Agriculture
3.1.1 Dehydrogenase (EC 1.1.1.48)
3.1.2 Phosphatase (EC 3.1.3.2)
3.1.3 β-glucosidase (EC 3.2.1.21)
3.1.4 Protease (EC 3.4)
3.1.5 Urease (EC 3.5.1.5)
3.2 Enzyme Assay
3.2.1 Dehydrogenase Assay
3.2.2 Phosphatase Assay
3.2.3 β-glucosidaseAssay
3.2.4 Protease Assay
3.2.5 Urease Assay
3.3 Factors Affecting Enzyme Assay
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
The last unit discussed the six classes of enzymes and their catalytic
functions. In this unit, you will learn of some enzymes that are of great
importance in agriculture. Enzyme activities are substrate specific and
specific in reactions, therefore one enzyme activity value alone cannot
give an overall picture of the soil status. Hence, measurement of various
enzymes will be more useful to evaluate biochemical activity and related
processes. The enzymes selected are mainly responsible for biochemical
processes in carbon, nitrogen and phosphorus cycles in soil.
2.0 OBJECTIVES
• explain the importance soil enzymes in agriculture

• discuss the reactions they catalyse
86
SLM 505 MODULE 4
• determine the enzymes reactions in soil.
3.0 MAIN CONTENT
3.1 Soil Enzymes Important in Agriculture
3.1.1 Dehydrogenase (EC 1.1.1.48)
Dehydrogenases are often measured because they are found only in

living systems, and are important to enzyme systems of all
microorganisms (that is, they are intracellular enzymes). They are
responsible for the oxidation – reduction reaction of soil organic matter
by transferring electrons or hydrogen from substrate to acceptors. Their
activity gives an indication of a good measure of microbial oxidative
activity. Therefore, dehydrogenases are used in evaluating metabolic
activity of soil microorganisms.
3.1.2 Phosphatase (EC 3.1.3.2)
There are two types of phosphatase enzymes namely acid phosphatase

and alkaline phosphatase. These enzymes are under the class of
hydrolase enzymes. They are good indicators of soil facility. They affect
the P-acquisation and P-use efficiency of plants and catalyse the
hydrolysis of P-ester bonds ad anhydrides of H3PO4 from the organic
matter resulting in the release of inorganic phosphorus. They hydrolyse
the P-ester bond of the P-nitrophenyl phosphate and then P-nitrophenol
is released. They are the key enzymes in P-cycling in soil and release
phosphorus (P) from both cellular and extracellular organic compounds
at different stress levels. Their activity is higher where higher quantity
of organic C is found. Management practices in mixed cultures which
include P stress in the rhizosphere may affect the secretion of these
enzymes. Understanding the activity of the enzyme is important for
predicting their interactions as their activities may in turn regulate
nutrient uptake and plant growth in soil.
3.1.3 Beta-Glucosidase(EC 3.2.1.21)
Beta (β)-glucosidase formerly known as gentiobiase or

cellobiasecatalyses the hydrolysis of β-glucosides such as B-D-
glucopyranosides and gives an idea about the decomposition of organic
matter. This enzyme is related with carbon cycle (C-cycle). This enzyme
87
converts cellulose to glucose which is an important energy source for

soil microorganisms. Cellulose is the most important organic compound
and its mineralisation and degradation in soil is a major process in the
carbon cycle. β-glucosidase activity therefore, is considered an indicator
for biomass turnover. This enzyme is more dominant in soils than Alpha
(α)-glucosidase.
3.1.4 Protease (ec 3.4)
This enzyme catalyses the hydrolysis of proteins (Proteolysis) which is

an important step in the organic nitrogen cycle (ammonification and
nitrification) of soils. It helps in the maintenance of soil fertility and
catalyse substrates with peptides. They reflect the proteolytic potential
of a soil and thus indicate the protein degradation capacity.
3.1.5 Urease (EC 3.5.1.5)
Urease (urea amidohydrolase) is the enzyme the catalyses the hydrolysis

of urea to CO2 (carbon dioxide) and ammonia (NH3)
NH2CONH2 + H2O CO2 + 2NH3
Urease acts on the C-N bonds other than the peptide bonds and two C-N
bond are broken in hydrolysis of urea. It is the first enzyme protein to be
crystallised. It is very widely distributed in nature and has been found in
microorganisms, plants and animals.
3.2 Enzyme Assay
When investigating enzyme reactions in soil, you must develop an assay

for the enzyme. Enzyme assay is the addition of a known amount of soil
to a solution containing a known concentration of substrate species and
determining the rate at which the substrate is converted to a product
under carefully controlled conditions of temperature, pH and ionic
strength.
1) Dehydrogenase assay
This method involves the release of tetrazoliumformazan when
soil is treated with tris-HCl buffer (pH 7.5) and INT solution
added (iodonitrotetrazolium chloride – INT) and kept at 40 oC for
one hour (1 hr). Then methanol is added and sample mixed and
left in the dark for some minutes. The INTF released is extracted
by filtration and determined spectrophotometrically.
2) Phosphatase assay
88
SLM 505 MODULE 4
This method involves the colorimetric estimation of the P-

nitrophenol released by phosphatase activity when soil is
incubated with buffered (pH 6.5 for acid phosphate activity and
pH 11 for alkaline phosphate activity) sodium P-nitrophenyl
phosphate solution and toluene at 37 oC for one hour. The
calcium chloride (CaCl2) and NaOH (sodium hydroxide) are
added and the soil suspension filtered.
3) β-glucosidase assay
The principles of this method are similar to that of phosphatase.
In this case P-nitrophenol is released by β-glucosidase when soil
is inculcated with buffered (pH 6.0) PNG solution (P-
nitrophenyl- β-D-glucoside and toluene at 37 oC for one hour.
The P-nitrophenol released is extracted by filtration after-addition
of CaCl2 and THAM buffer (pH 12) and determined
colorimetrically.
4) Protease assay
This method involves the release of Tyrosine when soil is treated
with casein denatured by heat and dissolved in Tris-HCl buffer
(pH 8) and incubated at 51 oC for one hour 30 minutes. Then
Tris-HCl and acetic acid are added. The amino acid formed is
extracted by filtration and determined colorimetrically.
5) Urease assay
The method designed for assay of urease under optimum
conditions are based on determination of the NH4+ (ammonium
ion) released when soil is incubated with THAM buffer
(Tris(hydroxymethyl) amino methane), urea solution and toluene
at 37 oC for two hours. The NH4+ released is determined by
treatment of the incubated soil sample with KCl (potassium
chloride) containing Ag2SO4 (silver sulphate) and steam
distillation with MgO for few minutes.
All the enzyme activities measured are expressed as micromole of

product released per hour per gram of soil used.
3.3 Factors Affecting Enzyme Assay
Soil treatments and methods of preparation have marked effect on the

results obtained in enzyme assays. Air-drying, storage conditions,
storage temperature and grinding affect enzyme assays. Preparation of
homogenous soil sample is essential because enzymes have been shown
to be unevenly distributed in the soil fractions. Shaking the soil substrate
mixture affects enzyme activities and should be put into consideration
when studying kinetics of enzyme reactions in soil.
89
4.0 CONCLUSION
From this unit, soil enzymes are potential indicators of soil quality
because of their role in soil biology, biochemical fertility of soil and
rapid response to changes in soil management. In conclusion, because
all biochemical transformations in soil are dependent on, or related to
the presence of enzymes, studying soil enzyme activities will give you
an insight into the biochemical processes in the soil.
5.0 SUMMARY
The enzymes and the reactions they catalyse are summarized in the table
below:
Enzyme Reaction
Dehydrogenase Oxidation of organic compound using hydrogen as
acceptor
INT + H+ INTF + HCl
Acid phosphatase Orthophosphoric monoester + H2O An alcohol +
orthophosphate
Β-glucosidase Hydrolysis of terminal, non-reducing β-D-glucose
residues with release of β-D-glucose
Protease Hydrolysis of proteins to petides and amino acids
Urease Hydrolysis of urea to CO2 and NH4+
6.0 TUTOR–MARKED ASSIGNMENT

1) Explain the importance soil enzymes in agriculture.
2) Discuss the reactions they catalyse.
3) Determine the enzymes reactions in soil.

(3rded.). Canada: Academic Press Publications,.
Nannipieri, P., Kandeler, E. &Ruggiero, P. (2002). Enzyme Activities

and Microbiological and Biochemical Processes in Soil. In: R.S.
Burns and R.P.
Dick (Ed.). “Enzymes in the Environment Activity, Ecology and

Applications. New York: Dekkers.
90
SLM 505 MODULE 4

Biochemistry.(3rded.)India, New York: New Delhi for Worth
Publishers..

Chemistry.(3rded.).Chichester, England: Horwood Publishing..
Price, N.C. &Stevens, L. (1999).Fundamentals of Enzymology. (3rded.).

Oxford: Oxford University Press,.

Terms.SSSA, Madison, WI.138pp. Available online at
91
UNIT 4 KINETICS OF ENZYME REACTIONS IN SOIL
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Theory of Enzyme Reactions in Soil
3.1.1 Derivation of Michaelis-Mention Equation
3.2 Transformation of MichaelisEquation
3.3 Factors Affecting Rates of Enzyme Reaction
3.3.1 Concentrations of Enzyme and Substrate
3.3.2 Temperature
3.3.3 pH
3.3.4 Cofactors, Inhibitors and Ionic Environment
3.4 Factors Affecting Enzyme Activities in Soil
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Two most important properties of enzymes are their specificity and

catalytic efficiency. This involves the velocities of chemical reactions of
the enzymes (chemical kinetics). The reaction of any enzyme is
measured by the rate of the chemical reaction being catalysed by the
enzyme. In this unit, you will learn about Michaelis-Menten theory of
enzyme reactions in soil and other transformations of the equation
derived from this theory. Also the factors affecting the rates of enzyme
reactions will be discussed.
2.0 OBJECTIVES
• explain the Michaelis-Menten theory of enzyme reactions

• derive the Michaelis-Menten equation and other transformations
of the equation
• discuss the factors affecting the rate of enzyme reactions.
92
SLM 505 MODULE 4
3.0 MAIN CONTENT
3.1 Theory of Enzyme Reactions in Soil
Enzymes are proteins that are specific in their reactions and catalytic
efficiency. The enzyme reactions called chemical kinetics because it
involves velocities of chemical reactions is measured by the rate of the
chemical, reaction being catalyzed by the enzyme. Equation describing
the kinetics of enzyme reactions in heterogenous system like soil is
given below:
K1K3
E +SK2 ES E + Product
Enzyme substrate Enzyme-substrate complex
This is a rate equation of enzyme with a single substrate where K1, K2,
K3 are velocity constants or rate constants of the three processes.
Generally, from the above equation, the complex of enzyme and
substrate is unstable and proceeds through a number of steps of
rearrangement to form the product plus the original enzyme. This theory
of enzyme action was proposed by Michaelis and Menten (1913).
3.1 Derivation of one Substrate Enzyme Catalyzed Reaction

(Michaelis-MentenEquation)
E+S ES…… (1)

K +1
ESK-1 E + P ..….. (2)
Assumption 1 by Michaelis-Menten
- Formation of ES complex
- Breakdown of ES complex
Assumption 2
- Reaction must be reversible
- Rate constant of forward and backward reactions have positive
and negative subscripts respectively
The initial velocity Vo = Rate of breakdown of ES complex

Vo = K + 2 [ES] …… (3), cannot be determined directly
d [ ES ]
Rate of formation of ES =
dt
d [ ES ]
= K + 1 [(ET) – (ES)][S] …. (4)
dt
93
Note: ET –ES = E1
d [ ES ]
= K – 1 [ES] + K +2 [ES] …… (5) Reverse reaction
dt
At steady state, rate of formation of ES = Rate of formation of ES
K + 1([ET] – [ES]) [S] = K – 1 [ES] + K + 2 [ES] …… (6)
Rearranging equation (6), you have

K −1+ K + 2
= Km (Michaelis constant) …… (7)
K +1
[ ET ][ S ]
[ES] = ……. (8)
Km + [ S ]
From equation (8) Vo = K + 2 [ES]

Vo
[ES] =
K +2
Substitute foe ES in equation (3), its value from equation 8 will be
K + 2[ ET ][ S ]
Vo = ……….. (9)
Km + [ S ]
K + 2 [ET] = Vmax………… (10)
V max .[ S ]
Therefore Vo = …….. Michaelis-Menten equation of ES
Km + [ S ]
complex
3.2 Transformation of MichaelisMentenEquation
V max .[ S ]
From the equation , three other linear transformations are
Km + [ S ]
obtained
1 1 Km 1
a) = + - This is called Linear Weaver Burk
V V max V max [ s]
Transformation
[S ] Km 1
b) = + .[ S ] - Hane-Wolf Transformation
V V max V max
V
c) V = V max − Km • - Eadie-Hofstee Transformation
[S ]
Plots of the above transformations give straight lines. Once the Km and
Vmaxare known for an enzyme reaction, the reaction velocity (V) can be
calculated for any substrate concentration. Km is important in estimating
the substrate concentration that will give Vmax.
94
SLM 505 MODULE 4
Disadvantages of LWB plot

(a) Line Weaver – Burk Plot When plotting V against [S], the graph appears to be a
rectangular hyperbolic curve. You cannot know when
you are approaching Vmax, hence you cannot
1 adequately calculate Km.
V
Slop= Km
V max 1) Because you are taking reciprocals
1 1
( and any small error will be magnified.
Intercept = 1 V [S ]
V max 2) There is clustering of the points when 1/V is plotted
against 1/[S]
1
[S ]
(b) Hane-Wolf Plot
Advantages of Hane and Eddie
1) Any small error in LWB will be magnified
[ S ] Slope= 1 since you are plotting 1/V against 1/[S], hence
Hanes and Eddie plots will correct the mistakes
V V max
or error.
2) Km can be calculated from the errors in LWB.
Intercept = Km
V max
-Km [S ]
(c) Eddie-Hofstee Plot

Advantages of Eddie Plot
Vmax 1) Km can be determined directly from
slope.
Slope = -Km 2) Vmax can be determined directly from
intercept
V
Intercept = V max
Km
V
[S ]
95
3.3 Factors Affecting Rates of Enzyme Reactions
3.3.1 Concentration of Enzyme and Substrate
Most enzyme catalyzed reactions are either zero order reaction (reaction
where the rate is constant and independent of substrate concentration) or
first-order reaction (reaction where the rate at any time is proportional to
the existing substrate concentration). Irrespective of the order of
reaction, the rate of reaction is proportional to the enzyme concentration.
Zero Excler Kinetics

Velocity Vmax
Vmax
2 1st Order Kinetics
Km = Michael’s Constant
Km [S]
The graph shows when the enzyme concentration is constant and the
substrate concentration vary over a wide range; the velocity of enzyme
catalyzed reaction is shown.
1) At low substrate concentration, the velocity of reaction follows a

first order reaction equation.
2) At higher substrate concentrations, a maximum velocity is
obtained independent of further amounts of substrate and this
follows a zero order reaction equation.
3) The magnitude of the Vmax (maximum velocity) is proportional
to the concentration of the enzyme. That is, the higher the
enzyme concentration, the higher the Vmax.
3.2.2 Temperature
The activity of any chemical reaction increases with temperature,

doubling for every 10 oC increase. The rate of enzyme reaction increases
until it reaches a maximum beyond which the rate reaction begins to
decrease due to enzyme inactivation. Enzyme catalyzed reactions are
less sensitive to temperature changes compared to uncatalysed reaction.
Enzyme catalyzed reaction rate increases by a factor of < 2. The
96
SLM 505 MODULE 4
dependence of temperature on the rate constant is described by

Arrhenius equation.
 Ea 
K = A exp  − 
 RT 
Where
A = Pre exponential factor
Ea = Activation energy
R = Gas constant
T = Temperature (oK)
The log form of the equation is written as
 − Ea 
Log K =   + log A
 2.303RT 
Log A and Ea are intercept and slope respectively of the graph of logK
1
on
T
3.2.3 pH
Enzymes being proteinaceous, show marked changes in ionisation due

to pH fluctuations, each enzyme has a pH value at which the rate of
reaction is optimal and below or above this optimum the rate is lower.
Therefore, the catalytic action of enzymes operates within a pH range.
Enzymes are more stable close to their optimum pH and are irreversibly
denatured at extremes in acidity or alkalinity. The use of buffer is
essential to maintain optimum pH for the reaction duration.
3.2.4 Cofactors, Activators, Inhibitors and Ionic environment
Many enzymes are not catalytically active except in combination with a

non-protein (cofactor) component. These non-protein components are
heat stable, dialysable substances of low molecular weight, cofactors are
activators, coenzymes and prosthetic groups.
Prosthetic groups are substances that are bound firmly to the enzyme.
Coenzymes are organic substances that are freely dissociable from
enzymes. Some enzymes are activated by inorganic ions are not
changed during the catalysed process but are required before the enzyme
can carry out the reaction. These are called activators.
Inhibitors are compounds that slow down the rate of an enzyme

catalysed reaction. There are many ways they can act:
1) Inhibitors usually form complexes with various enzyme forms
and thus lowers the amount of enzyme available for participation
in a normal sequence.
2) They can also inhibit by complexing the substrate
97
3) The product of a reaction can also inhibit by recombining with

the enzyme form that results from the dissociation of the product.
Thereby raises the steady state concentration of the enzyme form that
yields the products when it dissociates.
A dead end inhibitor is one which neither acts as substrate nor product
but forms complexes with one or more enzyme forms.
Salts (Ionic environment) also affect or show clear effects on enzyme
activity. Changes in electrolyte concentration cause changes in the
activity coefficients of the reactants and the activated complex. The
degree of ionization of acidic and basic groups in the protein molecule
may be changed by the presence of salts. All these effects may either
accelerate or slow down the catalytic activity of the enzyme.
3.4 Factors Affecting Enzyme Activities in Soil
Among the many factors previously mentioned that affect enzyme

activities, these factors listed below are included:
• Cropping history
• Soil amendments
• Environmental factors such as seasonal variations, rainfall
• Water logging (this affects Redox potential (Eh) and pH thereby
affecting enzyme activity)
• Vegetation
• Agricultural chemicals (fertilizers, pesticides)
• Industrial pollutants.
i. Why do all enzyme – catalyzed reactions show a pH optimum?

ii. State the advantages and disadvantages of any two of the
transformations of Michaelis equation.
iii. Using suitable diagram, distinguish between Hane-Wolf, Eddie
Hofstee and Lineweaver-Burk plots.
4.0 CONCLUSION
From the study enzymes are specialized proteins that combine with
specific substrate and specific activators. They are specific for the types
of reactions they carry out or participate in various physical and
chemical factors have been identified that affect enzyme reactions in
soil. These factors are concentrations of enzyme and substrate,
temperature, pH, cofactors, ionic strength of the environment, cropping
history, rainfall, vegetation type, agrochemicals and industrial
pollutants. All these factors depend on soil type, dose of chemical
applied and the conditions of the study area.
98
SLM 505 MODULE 4
5.0 SUMMARY
Graphical representation of factors affecting enzyme activity.
1)pH effects on enzyme activity 4) Effect of enzyme concentration
Maximum
Rate
4x 3x
2x 1x
Reaction
Rate No enzyme
pH Product
Optimum Formed
5 6 78 9 10 11
pH Range Time
2) Temperature effect 5) Effect of activator
Maximum Rate
Enzyme + activator
Product formed
Denaturation
Velocity Enzyme only
Optimum Temperature
Time
Temperature
3) Effect of substrate concentration 6) Effect of

inhibition
zero Order Kinetics

Vmax
Velocity Enzyme only
Product formed
Enzyme + inhibitor
Ymax 1st Order Kinetics
2
Km = Michael’s Constant
99
Km [S]
Time
6.0 TUTOR –MARKED ASSIGNMENT
1) Explain the Michaelis-Menten theory of enzyme reactions.

2) Derive the Michaelis-Menten equation and other
transformations of the equation.
3) Discuss the factors affecting the rate of enzyme reactions.

(3rded.).Canada: Academic Press Publications.

Publishing Agency.

Biochemistry.(3rded.). New York: India, New Delhi for Worth
Publishers.
Palmer, T. (2001). Enzymes: Biochemistry, Biotechnology and

Chemical Chemistry. (3rded.). Chichester, England.Horwood Publishing.
Price, N.C. &Stevens, L. (1999).Fundamentals of Emzymology. (3rded.).

Oxford: Oxford University Press.

100
SLM 505 MODULE 4
UNIT 5 ENZYME INHIBITION
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Definition and Functions of Inhibitors
3.2 Types of Enzyme Inhibition
3.2.1 Reversible Enzyme Inhibition
3.2.1.1Competitive Inhibition
3.2.1.2Uncompetitive Inhibition
3.2.1.3Non-Competitive or Mixed Inhibition
3.3 Irreversible Inhibition
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Soils receive a variety of organic and inorganic chemicals and some of

these compounds like fertilisers, pesticides, municipal and industrial
wastes are added as part of soil and crop management. Other compounds
such as salts of trace elements are added to soils as impurities in lime
and fertilisers and as industrial pollutants. These compounds inhibit and
slow down the rate of enzyme catalysed reactions.
2.0 OBJECTIVES
At the end of this unit, you should be able:
• explain an inhibitor and define enzyme inhibition

• discuss the various types of enzyme inhibition
• differentiate between the various types of enzyme inhibition
using suitable diagrams.
3.0 MAIN CONTENT

3.1 Definition and Functions of Inhibitors
3.1.1 Definition
An inhibitor is a compound that slows down the rate of an enzyme
catalysed reaction. The process is called inhibition. Enzyme inhibitors
are available in:
101
3.1.2 Functions of Enzyme Inhibition
a) Mechanism and pathway of enzyme catalysis

b) Substrate specificity of enzymes
c) The nature of final groups at active sites
d) Helping to determine the groups that can participate in
maintaining the active conformation or structure of the enzymes.
3.2 Types of Enzyme Inhibition
Enzyme inhibition has been classified into two namely reversible and
irreversible inhibitions.
3.2.1 Reversible Enzyme Inhibition
There are three major types of reversible enzyme inhibition. They are:
a) Competitive (binds with only enzyme)
b) Uncompetitive (inhibitor binds with ESC)
c) Noncompetitive or mixed inhibition (inhibitor binds with either
enzyme or ESC).
The reversible inhibition pattern can be distinguished by the effect of the

reaction kinetics on the enzyme. This is analysed based on Michaelis-
Menten equation. For valid kinetic analysis the inhibitor must react
rapidly and reversibly with the enzyme or with the enzyme-substrate
complex (ESC).
3.2.1.1CompetitiveInhibition
The inhibitor can combine with free enzyme in such a way that it
competes with the normal substrate for binding at the active sites. The
competitive inhibitor reacts reversibly to form enzyme-inhibitor
complex (EI) similar to ESC. The inhibitor molecule is not chemically
changed by the enzyme. The presence of competitive inhibitor increases
the apparent Km of substrate to achieve its maximum velocity.
Conversely, competitive inhibitor does not affect the rate of breakdown

of enzyme-substrate complex (ESC).
102
SLM 505 MODULE 4
1/V (a)
inhibition
Slope = Km
Vmax
(b) No inhibition
Slope = Km
Vmax
-1
Km1(intercept)
Vmax
Without
InhibitionWith inhibition 1/[S]
LWB Plot of Michaelis-MentenEquation Showing Competitive

Inhibition (A) in The Presence of Inhibitor.
3.2.1.2 UncompetitiveInhibition
The inhibitor does not combine with the free enzyme or affect its
reaction in normal substrate but combined with ESC to give an enzyme-
substrate inhibitor complex (ESI) which cannot undergo reaction to give
a product. From the graph below, this relationship suggests that degree
of inhibition may increase with increase in substrate concentration. This
type of inhibition can be recognised in the double reciprocal plot.
(a)
1/V
(
b)
Slope = Km
Vmax
Km
Constant
1(intercept)
Vmax Vmax, slope charge
- 1 1
Km [S]
103
The slope of the plot remains constant as the concentration of the

inhibitor increases. Uncompetitive inhibition is rare in one substrate
catalyzed reaction but is common in two substrate reaction.
3.2.1.3 Non-competitive or Mixed Inhibition
It can interfere with the free enzyme or with the ESC (that is, a
noncompetitive inhibitor) interfering with the action of growth. This
inhibitor binds to a site on the enzyme other than the active site with the
sole effect of deforming the enzyme. So it does not form the enzyme
substrate complex (ESC) or if formed cannot decompose at the normal
rate to form the product. These effects are not reversed by increasing
substrate concentration. The inhibition reaction results in two inactive
forms of EI complex and ESI complex. Some enzymes that require
metal ions for activity are inhibited non competitively by agents capable
of binding metal ion.
1/V Km = Slope
Inhibitor Vmax
inhibitor No
Inhibitor
1 (intercept)
Vmax Km =
Slope
Vmax
(I
1/vmax (Intercept) No Inhibitor
- 1 1
Km [S]
LWB-plots of Michaelis-Menten equation showing Non-competitive or

mixed inhibition (a) in the presence of inhibitor and (b) in the absence of
inhibitor.
3.3 Irreversible Inhibition
Some enzymes undergo irreversible inhibition when they are treated

with agents that can covalently and permanently modify their final
groups which is needed for catalysis. As a result, the enzyme molecule
104
SLM 505 MODULE 4
becomes inactive. Irreversible inhibition cannot follow Michaelis-

Menten principles which assume reversible formalism. Irreversible
inhibitors are very valuable in mapping of active sites.
4.0 CONCLUSION
From this unit, you have learnt that an inhibitor slows down the rate of
an enzyme catalyzed reaction by complexing with the enzyme or
substrate or the product recombines with the enzyme. Two types of
enzyme inhibition were identified namely reversible and irreversible
inhibition and the reversible inhibition consisted of three major types,
competitive, uncompetitive and Non-competitive or mixed inhibitions.
5.0 SUMMARY
The table below summarises the effect of the inhibitors on the

Lineweaver-Burk (LWB) plot
Inhibition Slope Intercept

No inhibition Km 1
V max V max
Competitive Km  [1]  1
1 + 
V max  KI  V max
Uncompetitive Km 1  [1] 
1 + 
V max V max  KI 
Mixed or Km  [1]  1  [1] 

1 +  1 + 
Noncompetitive V max  KI  V max  KI 
7.0TUTOR-MARKED ASSIGNMENT
1. Explain an inhibitor and define enzyme inhibition.

2. Discuss the various types of enzyme inhibition.
3. Differentiate between the various types of enzyme inhibition
using suitable diagrams.
Eldor, A.P. (Ed.). (2007). Soil Microbiology, Ecology and

Biochemistry. (3rd ed.). Canada:Academic Press Publications

Publishing Agency..
105
Nelson, D.L. &Cox, M.M. (2002). Lehninger Principles of

Biochemistry. (3rd ed.).New York:India, New Delhi for Worth
Publishers.
Palmer, T. (2001). Enzymes: Biochemistry, Biotechnology and

Chemical Chemistry. (3rd ed.).Horwood Publishing, Chichester,
England.
Price, N.C. &Stevens, L. (1999).Fundamentals of Enzymology. (3rd ed.).

Oxford: Oxford University Press,.

terms.SSSA, Madison, WI.138pp. Available Online at
106
MODULE 5 PESTICIDES IN SOIL
Unit 1 Nature of Pesticides

Unit 2 Behavior of Pesticides in Soil
Unit 3 Effect of Pesticides on Soil Organism
Unit 4 Biodegradation of Pesticides
Unit 5 Pesticide Persistence in Soil
UNIT 1 NATURE OF PESTICIDES
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 What are Pesticides?
3.2 Classification of Pesticides
3.2.1 Classification Based on Target Organism
3.2.2 Classification Based on Mode of Action
3.3 Types of Pesticides
3.3.1 Insecticides
3.3.2 Fungicides
3.3.3 Herbicides
3.3.4 Nematicides
3.3.5 Molluscides
3.3.6 Rodenticides/Alkalicides
3.4 Benefits and Cost of Pesticides
3.4.1 Benefits of Pesticides
3.4.2 Cost of Pesticides
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
A lot of synthetic organic compounds are manufactured yearly such as

plastics, plasticisers, lubricants, refrigerants, fuels, solvents,
preservatives and pesticides. Some of these organic compounds or
chemicals are extremely toxic to microbes and humans while some are
inactive and harmless. These synthetic organic chemicals are found
everywhere in our environment (soil, groundwater, plants and even our
bodies). They reach our environmentaccidentally through leakage and
spills, planned spraying as is done on our agricultural fields, or by other
treatments. Pesticides are therefore synthetic organic chemicals designed
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to kill pests (any organism that the pesticide user see to be damaging).
Hence, in this unit, you will be looking at the nature of pesticides, their
benefits and costs, behavior in soil, effects of soil organisms and their
persistence.
2.0 OBJECTIVES
• explain the nature of pesticides

• discuss the benefits and costs of pesticides
• differentiate between the various types of pesticides.
3.0 MAIN CONTENT
3.1 What are Pesticides?
Pesticides have become the most widespread organic pollutants

associated with soils. Pesticides are synthetic organic chemicals
designed to kill or inhibit pests. A pest is any organism that the pesticide
users see to be damaging. When pesticides are applied, those that find
their way into the soil may inhibit or kill soil organisms resulting in the
imbalance of the soil community. Others may be transported from the
soil to air, water or vegetation (plants) where they may be contacted,
inhaled or ingested by some organisms. Therefore, it is important to
control the release of these organic chemicals and know their fate
(behavior/mode of action) and effects in the soil. Some may enter as
contaminants from industrial organic wastes applied or spilled on soils
as components of machine parts thrown away, lubricants or as
agrochemicals (pesticides) applied to agricultural fields.
For those meant to be applied on plants as pesticides, most of it reaches

the soil because they have missed the insect or plant leaf that was the
target (purpose) of the application. Hence, they are the most widely
causes of organic pollutants connected with soils.
3.2 Classification of Pesticides
Pesticides are classified into two:

1) Based on their target (pest) organisms
2) Mode of action
3.2.1 Classification Based on Target Organism
Pesticides under this group are namely:

a) Insecticides – insect killers
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b) Fungicides – fungi killers

c) Herbicides – weed killers
d) Rodenticides or Alkalicides – mice or rodent killers
e) Nematicides – nematode killers
f) Molluscides – snails or slugs/Mollucs killers
g) Bactericides – bacteria killers.
The first three are used in large quantities and are therefore more likely
to contaminate the soil. Most pesticides contain aromatic rings of some
kind.
3.2.2 Classification Based on Mode of Action
Pesticides are further divided into two main groups based on their mode
of action namely:
a) Contact pesticides
b) Systemic pesticides.
3.2.2.1 Contact Pesticides
These pesticides do not penetrate into the tissue and therefore are not
translocated within the vascular system or tissue or transport system of
the target plant. They are susceptible to weather effects and cannot stop
infection once infection has begun or started to spread through plant
tissues. They are only protectants, example: cypermethrin designed to
prevent insect attack on cowpea during flowering and podding stages of
growth and fungicide designed to prevent seed rot, example: Benomyl
(Benlate).
3.2.2.2 Systemic Pesticides

These pesticides effectively penetrate the cuticle and move through the
plant vascular system. Example: Benomy (benlate) is a fungicide
chemotherapeutant. It not only protects from fungal attack but cures and
inhibits any established infection.
Systemic pesticides have three qualities namely:

a) Those that are not absorbed – protectants
b) Those absorbed but not translocated – chemotherapeutants
c) Those absorbed and translocated which are the main systemic
pesticides.
3.3 Types of Pesticides
3.3.1 Insecticides
There are three general groups here namely:
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a) The chlorinated hydrocarbons

Example: DDT
DDT was the most extensively used insecticide in this group until
banned due to its low biodegradability and persistence as well as
toxicity to birds and fish.
b) The organophosphates
They are generally biodegradable and less likely to build up in
soils and water but they are extremely toxic to humans, hence
great care must be used in handling and applying them. Example:
Parathion.
c) The Carbamates
They are the least dangerous because they are readily/rapidly
biodegradable and have relatively low mammalian toxicity but
highly toxic to honeybees and other beneficial insects and
earthworms. Example: Carbaryl.
3.3.2 Fungicides
Fungicides are mainly used to control diseases of fruits and vegetable

crops and also used as seed coating (dressing) to protect against seed rot
(Benlate (Benomyl)). Some are used to protect harvested fruits and
vegetables from decay andto prevent wood decay and to protect
clothings from mildew. Examples: Thiocarbamates and Triazoles are
currently in use.
3.3.3 Herbicides
The amount of herbicides used is much compared to insecticides and

fungicides combined. Most herbicides are biodegradable and relatively
low in mammalian toxicity but some are quite toxic to fish and other
wildlife.
Also, they can have adverse effects on beneficial aquatic vegetation that
provide food and habitat for fish and shell fish.
Examples:
a) The Triazines – Atrazine used for the control of weed in corn.
b) Substituted ureas – Linuron
c) Some carbamates
d) The relatively new sulphonylureas – Nicosulphuron. They are
potent (very effective) at very low rates
e) Dinitroanilines – Trifluralin
f) Acetanilides – Alachlor (This is quite mobile in the
environment).
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3.3.4 Nematicides
Some of them are known to contaminate soils and water draining from
treated soils. Examples: Some carbamates used as nematicides are quite
soluble in water, not adsorbed by soil (clay particles) and hence leached
downwards and into the ground water.
3.3.5 Molluscides
They are used for the killing of slugs and snails.
3.3.6 Rodenticides/Alkalicides
They are used for the killing of mice or rodents such as rats. Quite a
number of rat killers are found in the market.
3.4 Benefits and cost of Pesticides
3.4.1 Benefits of Pesticides
Pesticides have provided many benefits to the society such as:

1) Control of mosquitoes and other vectors that cause human
diseases such as yellow fever and malaria.
2) Protect crops and livestocks against insect pests and diseases.
3) Control weeds by the use of herbicides without which
conservation tillage (especially no-tillage/zero tillage) would be
much difficult to adopt.
4) Much of the progress made in controlling soil erosion would not
have come about without herbicide.
5) They reduce food spoilage from farms or fields (that is, they are
used for storage of food and grains).
6) Biological nitrogen fixation process is enhanced (stimulated) by
some pesticide use by reducing protozoa activity and other
competitors or predators of nitrogen fixing bacteria.
3.4.2 Cost of Pesticides
As the benefits to society are great, so are the costs. Pesticides should
not be seen as something you cannot do without (indispensible), because
some farmers produce profitable yields without the use of pesticides.
Even with the use of pesticides, insects, diseases and weeds still cause
crop loss. Therefore, the use of large amount/quantities of pesticides
cause:
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1) Imbalance in microbial community: Though they are designed to

kill living things, many are potentially toxic to organisms other
than the pests for which they are intended.
2) Detrimental to beneficial insects (butterflies, bees, etc) and
certain soil organisms (Rhizobium, nitrifying bacteria).
3) Fungicides especially fumigants have adverse effect on soil fungi
and actinomycetes thereby slowing down the humus formation in
soil.
4) They cause health hazards to humans and animals. Those that do
not quickly breakdown may be biologically magnified (i.e.
increased) as they move up the food chain, for instance,
earthworms ingest contaminated soil and the chemicals tend to
concentrate in their bodies. When birds and fish eat them, the
pesticides build up to lethal levels.
5) The near extinction of certain birds of prey is as a result of the
devastating environmental pollution consequences of pesticide
use.
6) Studies have shown that human hormone balance (endocrine)
may be disrupted by small traces of some pesticides found in
water, food and air.
1. Explain the nature of pesticides.

2. Discuss the benefits and costs of pesticides.
3. Differentiate between the various types of pesticides.
4.0 CONCLUSION
From our study or discussions in this unit, pesticides are synthetic

organic compounds and classified into about seven groups based on
their target organisms and into two major groups based on their mode of
action. They are beneficial to the society and soil organisms and at the
same time have detrimental effects; hence care must be taken to control
the release of pesticides.
5.0 SUMMARY
In this unit we have learnt that pesticides are classified in broad terms as
insecticide, fungicides, herbicides, nematicides, molluscides,
rodenticides (alkalicides) and bactericides used to control or inhibit
insect pests and diseases. In terms of mode of action, they are classified
as contact and systemic pesticides.
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They have provided many benefits but also have adverse effects on both
humans and microorganisms, hence you must exercise caution in the use
of pesticides.
1. Explain the nature of pesticides.

2. Discuss the benefits and costs of pesticides.
3. Differentiate between the various types of pesticides.
Alexander, M. (1994).Biodegradation and Bioremediation.New

York:Wiley.

(3rded.).Canada: Academic Press Publications.

Microbiology.California: Academic Press, San Diego.

112
SLM 505 MODULE 5
UNIT 2 BEHAVIOR OF PESTICIDES IN SOIL
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Fate of Pesticides in Soil
3.1.1 Volatility
3.1.2 Adsorption
3.1.3 Leaching and Runoff
3.1.4 Contamination of Groundwater
3.1.5 Chemical Reactions
3.1.6 Plant Absorption
3.1.7 Microbial Metabolism
3.2 Biodegradation of Pesticides
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Once pesticides reach the soil, they move in one or more ways from the
soil to the air, water or vegetation (plants) where they may be contacted,
inhaled or ingested by some organisms. Therefore, it is important to
control their release and know their fate (behavior or mode of action)
and effects in soil.
2.0 OBJECTIVES
• identify the various ways in which pesticides move in soil

• discuss or explain these various modes of action in soil.
3.0 MAIN CONTENT
3.1 Fate of Pesticides in Soil
Once pesticides reach the soil, they move in one or more ways such as:
1) They may vaporise into the atmosphere without chemical charge.

2) They may be adsorbed by soil particles like silicate clays.
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3) They may move downwards through the soil in liquid or solution

form and be lost from soil by leaching into underground water.
4) They may undergo chemical reactions within or on the soil
surface.
5) They may be broken down by soil microorganism.
6) They may wash into streams and rivers in surface runoff and
leaching.
7) They may be taken up by plants or soil animals (organisms) and
move up the food chain.
Note that the specific fate of these pesticides is determined at least in

part by their chemical structures, which are highly variable.
3.1.1 Volatility
Pesticides vary in their volatility and susceptibility to atmospheric loss.

Example, fumigants like methyl bromide (now banned) was selected
because of its high vapour pressure that allows it to penetrate the soil
pores to reach the target organisms.
But this encourages rapid loss to the atmosphere after treatment, unless
the soil is covered or sealed. A few herbicides (Trifluralin) and
fungicides (Pentachloro nitrobenzene -PCN B) are volatile and make
vaporization their primary means of loss from soil.
3.1.2 Adsorption
This depends on the characteristics (structure) of the compound and the

soil type to which they are added. For instance, soils high in organic
matter and soils with high surface area clays tend to be the strongest
adsorbents for some compounds while soils with oxide coatings on soil
particles strongly adsorb others. The presence of functional groups like
OH, NH2, NHR, CONH2, COOR and +NR3 in the chemical structure
encourages adsorption especially on the soil humus. Hydrogen bonding
and protonation (addition of H+ to a group such as an –NH2 (amino)
group) promotes some of the adsorption. Large organic molecules with
many charged sites are more strongly adsorbed. Herbicides like Diaquat
and Paraquat with positively charged groups are strongly adsorbed by
silicate clays. Adsorption by clays of some pesticides is pH dependent
with maximum adsorption at low pH, thus encouraging protonation.
3.1.3 Leaching and Runoff
The rate of leaching from soil depends on their solubility in water and
their potential for adsorption. Example: Chloroform and Phenoxyacetic
acid are more water soluble than DDT (1,1 – Trichloro 2,2 bis 4-
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SLM 505 MODULE 5
chlorophenyl ethane) and Pentachloro benzene (PCB) which are soluble

in oil but not in water. High water solubility favours leaching losses
while strongly adsorbed molecules are not likely to move down the
profile. Hence, conditions that favour adsorption discourage leaching.
The greatest leaching occurs in highly permeable sandy soils that are
low in organic matter. High rainfall periods at the time of application
promote leaching and runoff losses. Herbicides are more mobile than
fungicides and/or insecticides and therefore more likely to find their way
to groundwater supplies and streams.
3.1.4 Contamination of Groundwater
Pesticides reach the groundwater through accidental spillage and from

normal agricultural use. Many people depend on ground water (well
water) for their drinking supply; therefore leaching of pesticides is of
great concern because the amount of pesticides discovered in drinking
water was found to be high.
3.1.5 Chemical Reactions
Some pesticides undergo chemical modification independent of soil

organisms once they get in contact with soil. Examples are:
1) Fe-cyanide decompose within hours or days on exposure to bright
sunlight
2) DDT, Diquat and Triazines photo-decompose slowly in sunlight.
3) Triazine herbicides (example: Atrazine) and organophosphate
insecticides (example: Malathion) undergo hydrolysis and
subsequent degradation. Therefore, degradation independent of
soil organisms does occur.
3.1.6 Plant bsorption
Pesticides are commonly absorbed by higher plants especially systemic

insecticides and most herbicides because they are taken up to perform
their intended function. The absorbed chemical may remain inside the
plant or be broken down (degraded). Some of the products of
degradation may be harmless or toxic than the original chemical
absorbed. Those that remain on the plant parts whether as fresh fruits
and vegetables or as processed food became of concern to the
society.Hence, the strict regulation of the use of pesticide residues in
food to ensure human safety by regulatory agencies.
3.1.7 Microbial Metabolism
115
This is the most important method by which pesticides are removed

from soils (biochemically degraded  biodegradation). Polar groups like
–OH, COO- and –NH2 provide points of attack for the organisms.
Insecticides such as DDT and other chlorinated hydrocarbons like

Aldrin, Dieldrin and Heptachlor are degraded slowly and persist in soil
for long (about 20 years or more). Organophosphates (Parathion) are
degraded rapidly by a number of organisms. Herbicides like 2, 4-D,
Phenylureas, Aliphatic acids and Carbamates are readily attacked by a
host of organisms but Triazines are slowly degraded mainly by chemical
action.
Most fungicides depend on microbial degradation (decomposition)

though their rate of breakdown is slow causing residue problems.
Enumerate the fate of pesticides in soil and discuss microbial

metabolism of pesticides.
4.0 CONCLUSION
From our discussion in this unit, pesticides once they reach the soil,
behave in seven different ways namely volatilization, adsorption,
leaching and runoff, groundwater contamination, chemical reactions,
plant absorption and microbial metabolism, where they may be
contacted, inhaled or ingested by some organisms. Therefore, in
conclusion, it is important to control their release having known their
fate (behavior/mode of action) in soil as they are the most widespread
synthetic organic chemicals associated with soil.
5.0 SUMMARY
In summary, most of the pesticide applied in agricultural soils finds their

way through or into the soil in one or several ways namely through:
• Volatilisation
• Adsorption
• Leaching and runoff
• Contamination of groundwater
• Chemical reactions
• Plant absorption
• Microbial metabolism
Therefore, knowing their mode of action will help to control their

release in order to minimise environmental pollution, health hazards on
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SLM 505 MODULE 5
both humans and soil organisms. Therefore, the knowledge of pesticides

behavior will be of great importance in agricultural production.
117
1) Identify the various ways in which pesticides move in soil.

2) Discuss or explain these various modes of action in
soil.
Alexander, M. (1994).Biodegradation and Bioremediation.New York.

Wiley.

(13thed,).Prentice Hall, Upper Saddle River, NJ.

(3rded.).Canada:Academic Press Publications,.

Microbiology.San Diego, California.:Academic Press.

118
SLM 505 MODULE 5
UNIT 3 EFFECT OF PESTICIDES ON SOIL

ORGANISM
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Effect of Pesticides on Soil Organisms
3.1.1 Detrimental Effects of Pesticides on Soil
Organisms
3.1.2 Effects of Pesticides on Beneficial Soil Organism
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Most of the pesticides meant to be applied on plants missed the insect or

plant leaf that was the target of application and reach the soil. The soil is
the habitat for diversity of organisms. These pesticides vary in their
effects on soil ecology (soil microorganisms). Their effects could be
detrimental or beneficial.
2.0 OBJECTIVES

• discuss how pesticides adversely affect various soil organisms
• explain the effects of pesticides on the beneficial soil
microorganism.
3.0 MAIN CONTENT
3.1 Effect of Pesticides on Soil Organisms
3.1.1 Detrimental Effects of Pesticides on Soil Organisms
Pesticides vary widely in their effects on soil ecology (soil organisms)

and this in turn affects plant growth. Some of the major effects of
pesticides on soil organisms are:
• Imbalance in the soil ecology especially on soil microorganisms
(microflora)
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• Detrimental (adverse) effects on the fertility of the soil and crop

productivity
• Adverse effect on nitrification and nitrogen fixation by affecting
the bacteria responsible for these processes, e.g. Rhizobium,
Azotobacter, Nitrosomonas, Nitrobacter. Insecticides and
fungicides affect both processes more than most herbicides.Thus,
the soil Nitrogen balance is altered.
• Symbiotic (mutualistic) associations in soil are adversely affected
such as mycorrhiza association and root nodulation in legumes
• Rhizosphere microorganisms are altered due to the changes in the
soil physical to chemical properties.
• Fungicides especially fumigants affect adversely the fungi and
actinomycetes activities thereby slowing down the humus
formation in soil.
The negative effects of most pesticides on the beneficial soil

microorganisms are temporary and after a few days or weeks, organism
numbers recover. Hence, care must be taken to apply them when
alternative means of pest management are not available.
3.1.2 Effects of Pesticides on Beneficial Soil Organism
1) The bacterial levels in the soil are not so badly affected by

pesticides but the organisms (bacteria) responsible for
nitrification and nitrogen fixation are badly affected sometimes.
For instance, insecticides and fungicides affect both processes
more than most herbicides though some of the later (herbicides)
can reduce the number of organisms (population) carrying out
these two reactions.
2) Studies have shown that some pesticides enhance biological
nitrogen fixation (BNF) by reducing the activity of protozoa and
other competitors or predators of nitrogen fixing bacteria.
3) Ammonification is enhanced (stimulated) as a result of the above
(2 above).
In what ways do pesticides affect soil organisms?
4.0 CONCLUSION
From our discussions in this study, it can be concluded that pesticides

have detrimental effects on most soil organisms, especially on the
beneficial soil organism responsible for nitrification and nitrogen
fixation. They also affect or slow down soil formation by adversely
affecting fungi and actinomycetes activities. Studies have also shown
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SLM 505 MODULE 5
that pesticides enhance BNF by reducing the activities of the

competitors and predators (protozoa) of nitrogen fixing bacteria
resulting in increased ammonification process.
5.0 SUMMARY
From our study, we have learnt that pesticides have effect on the soil
microbial ecology. Their effects were both beneficial and detrimental to
soil organisms and to the soil itself by adversely affecting fungi and
actinomycetes activities in soil formation.
1) Discuss how pesticides adversely affect various soil organisms.

2) Explain the effects of pesticides on the beneficial soil
microorganism.
Alexander, M. (1994).Biodegradation and Bioremediation., New York:.

Wiley

(13thed.).Upper Saddle River, NJ:.Prentice Hall,

(3rded).Canada: Academic Press Publications.

Microbiology.San Diego, California: Academic Press.


(2nded,).New Jersey:Prentice Hall, Upper Saddle River,
121
UNIT 4 BIODEGRADATION OF PESTICIDES
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 What is Biodegradation?
3.1.1 Conditions that FavourBiodegradation
3.2 Reactions of Biodegradation
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
Pesticides applied on plant leaves in agricultural fields directly or

indirectly reach the soil. The ability and effectiveness of the soil to
degrade the toxic organic compounds to nontoxic compounds depends
on the physical, chemical and biological properties of the soil. The
biological properties (soil microorganisms) play the most important role
in pesticide degradation. This process of pesticide degradation by soil
organisms is called “Biodegradation”. It is important to note that all
pesticides are not biodegradable as shown in Unit 2 – fate of pesticides
in soil. Those that resist biodegradation are called “recalcitrant”.
2.0 OBJECTIVES
• explain biodegradation
• discuss the various reactions of biodegradation
3.0 MAIN CONTENT
3.1 What is Biodegradation?
Pesticides in soil are turned into nontoxic compounds by soil microbes.

Because the process takes place in soil, it is affected by several soil
factors such as organic matter content, moisture, temperature, pH
including microbes (microorganisms). These soil factors are essential in
the degradation of pesticides applied into soil. Pesticides degrade faster
under tropical (warmer) climate compared to temperate (cooler) climate.
Studies show that most organic pesticides degrade within 3 – 6 months
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under warm conditions. Soil organisms such as bacteria, fungi and

actinomycetes play most of the role in pesticide degradation in soil.
3.1.1 Conditions Favourable for Biodegradation
The following conditions have been observed or reported for proper and
good biodegradation of pesticides in soil:
1) The soil must be favourable for microbial and plant growth as
well as for enzyme activity.
2) The soil organism carrying out the degradation process must have
the needed catabolic activity in order to lower the concentration
of the contaminant.
3) The contaminant must be biologically available (i.e. must have
life in it).
4) The disadvantages of bioremediation must be less than the
process of removal of contaminant (biodegradation).
3.2 Other Reactions of Biodegradation
Other reactions that take place during biodegradation are:

1) Detoxification:
This is the process whereby the toxic compounds in a pesticide
are converted to nontoxic compounds. This reaction takes place
without the help of microorganisms.
2) Degradation:
This is the breakdown of toxic complex compound into simple
products through the process of mineralisation. Degradation and
mineralisation go together.
3) Conjugation:
Here the microorganism makes the substrate more complex or
combines the pesticide with the cell metabolites.
4) Activation:
This is the conversion of nontoxic substance a toxic compound
5) Change in toxicity spectrum:
Here the pesticide is metabolized into products inhibitory to other
organisms.
What is biodegradation and recalcitrant?
4.0 CONCLUSION
From our discussion in this unit, soil microorganisms play the most
important role in biodegradation, though not all pesticides are
biodegradable. Biodegradation of pesticides are affected by soil factors
123
hence the soil must be favourable for microbial and plant growth as well
as enzymatic activity.
The microorganisms must have catabolic activity to lower the

concentration of the contaminant. Other reactions apart from
degradation by microorganisms that take place are detoxification,
conjugation, activation and change in toxicity spectrum. In conclusion,
the ability of soil to properly degrade pesticides depends on the physical,
chemical and biological properties of soil.
5.0 SUMMARY
In this unit, you have learnt that the ability of the soil to degrade
pesticides properly depends on the soil factors including soil
microorganisms. Most pesticide degradation are carried out by soil
organisms, though there are exceptions. The soil condition must be
favourable for proper and good degradation to take place. Other
reactions reported to take place during biodegradation were discussed
such as detoxification, conjugation, activation and change in toxicity
spectrum.
1) Explain biodegradation.
2) Discuss the various reactions of biodegradation.
Alexander, M. (1994).Biodegradation and Bioremediation.New York.:

Wiley.


Microbiology.California: Academic Press, San Diego,


(2nded.).New Jersey: Prentice Hall, Upper Saddle River.
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SLM 505 MODULE 5
UNIT 5 PESTICIDE PERSISTENCE IN SOIL
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 What do you meanby Pesticide Persistence?
3.2 Effects of Pesticides Persistence in Soil
4.0 Conclusion
5.0 Summary
1.0 INTRODUCTION
The persistence of pesticides in the soil is a summation of all the

reactions, movements, and degradations affecting the pesticides.
Majority of pesticides degrade rapidly to prevent build-up in soils with
normal annual (yearly) applications. Those that resist biodegradation
cause environmental damage mostly. Continuous use of the same
pesticide on the same land (especially on agricultural lands) can increase
the rate of microbial (microorganisms) breakdown of that pesticides.
This is because there will be a population build-up of those
microorganisms with the enzymes needed to breakdown the compound.
This is an advantage but the breakdown sometimes may become rapid to
reduce pesticide effectiveness.
2.0 OBJECTIVES
• explain what pesticide persistence means

• enumerate the effects of persistence of pesticides in soil.
3.0 MAIN CONTENT
3.1 What Do You Mean By Pesticide Persistence?
When we talk of pesticide persistence, we mean how long it takes the

pesticide in question to breakdown to its nontoxic compounds that will
no longer be effective on the target (i.e. the purpose for which it is
applied) organism.
125
Persistence of pesticide therefore, is the summation of all the reactions,

movements and degradations affecting the pesticide(s). Some pesticides
degrade rapidly while others take long periods (even years) depending
on the chemical structure (especially the functional group) and
properties of the organic compounds in the pesticide.
3.2 Effects of Pesticides Persistence in Soil
When a pesticide persists longer than expected in soil, it could result

(lead) to:
1) Chronic health hazards: When pesticides are taken up
(assimilated) by plants, they move up the food chain and
accumulate to toxic levels as root tubers and leaves. When eaten
by humans or livestocks, it would lead to chronic health
problems.
2) Toxicity to microorganisms in soil: Accumulation of the organic
compounds in a pesticide to a level that becomes toxic to
microorganisms thereby inhibiting microbial activity in soil or
resulting in the death of the microbes.
3) Contamination of ground water, streams, and rivers: Some
pesticides reach the streams, rivers and underground water (well
waters) through accidental spillage or pesticides applied to land
ecosystems. The amount of pesticides so far discovered in
drinking water was found to be high and this has been of great
concern health wise. Some of the effects observed is the
discoloration of teeth and food poisoning (when the water is used
for cooking).
4) Environmental pollution: It could lead to environmental pollution
especially those that resist biodegradation (recalcitrants), that are
mostly chemically broken down by chemical reactions and
volatilization processes.
There are clear differences in their persistence and this varies from a few
days to years depending on the chemical structure and properties of the
organic compound in the pesticide.
For instance,
1) Organophosphate insecticides may last only a few days in soils.
2) 2, 4-D persist for only 2 – 4 weeks
3) PCBs, DDT, Aldrin, Chlordane, Mercurial fungicides and
Chlorinated hydrocarbons persist for 3 – 20 years or longer. DDT
and Mercurial fungicides (used for the control of insect pests on
agricultural fields) persists longer than expected. DDT (was the
most extensively used insecticide) and Mercurial fungicides were
banned due to their low biodegradability and persistence as well
as toxicity, leading to food contamination and adverse health
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hazards. Hence they are banned to use in agriculture and public

health departments.
4.0 CONCLUSION
In this unit and from our discussions organophosphate pesticides

degrade rapidly compared to all the other pesticides such as the
chlorinated hydrocarbons. They are found or observed to degrade within
few days to weeks while chlorinated hydrocarbons persist up to 3 – 20
years and even longer.
The persistence of pesticides has resulted in many health, hazards,

environmental pollutions and agricultural problems (due to their effects
on the beneficial microorganisms). Therefore, care must be taken in the
use or application of pesticides as how long a pesticide persists in soil is
important in pest management and environmental pollution.
5.0 SUMMARY
From the study of persistence of pesticides in soil, a range of persistence

of a number of pesticides is given below:
Pesticide Persistence
1) Chlorinated hydrocarbon insecticides 3 – 20 years
(DDT, chlordame, Aldrin, Dieldrin)
2) PCBs 2 – 10 years
3) Triazine herbicides (Atrazine, Simazine) 1 – 2 years
4) Benzoic acid herbicides (Amiben and 2 – 12 months
Dicamba)
5) Urea herbicides (Monuron, Diuron) 2 – 10 months
6) Vinyl chloride 1 – 5 months
7) Phenoxy herbicides (2, 4-D, 2,4,5-T) 1 – 5 months
8) Organophosphate insecticides 1 – 3 months (1– 12
(malathion, diazinon) weeks)
9) Carbamate insecticides 1 – 2 months (1-8
weeks)
10) Carbamate herbicides (Barban, (IPC) 2 – 8 weeks
Adapted from
1) Explain what pesticide persistence means.

2) Enumerate and discuss the effects of persistence of pesticides
in soil.
.
127
Alexander, M. (1994).Biodegradation and Bioremediation.New

York:John Wiley and Sons,.

Soils.(13thed.), Prentice Hall, Upper Saddle River, NJ..



(2005).Principles and Applications of Soil Microbiology. (2nd
ed.), New Jersey: Prentice Hall, Upper Saddle River.
128

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COURSE

Course Team Dr. Nkechi N.M. Chinke(Course Writer) -

NATIONAL OPEN UNIVERSITY OF NIGERIA

© 2023 by NOUN Press

All rights reserved. No part of this book may be reproduced, in any

Printed 2017, 2023

WHAT YOU WILL LEARN IN THIS COURSE

The overall aim of this course is for you to have a comprehensive

The aim of the course is to give you a better and comprehensive

• Introducing you to the origin and contributions of soil

Below are the broader objectives of the course, as a whole. By meeting

• explain enzyme kinetics and the transformations of Michaelis-

WORKING THROUGH THIS COURSE

The major components of the course include the following:

There are 25 study units in this course as follows:

Unit 1 Introduction and Brief History of Soil Microbiology

Unit 2 Introduction to Soil Biochemistry

Module 2 Microbiology of the Rhizosphere and Microbial

Module 3 Microbial Transformations of Cycles in Soil

Unit 1 Soil Organic Matter Transformation

Module 4 Soil Enzymes

Unit 1 What are Enzymes?

Module 5 Pesticides in Soil

Unit 1 Nature of Pesticides

Text Books and References

The assignments must be submitted to your tutor for formal assessment

TUTOR – MARKED ASSIGNMENT

You are advised to submit your assignments as required. Each

FINAL EXAMINATION AND GRADING

COURSE MARKING SCHEME

The following table shows how the marking scheme is divided.

Table 1: Course Marking Scheme

Table 2: Course schedule

Units Title of Work Weeks Assessment (end

Units Title of Work Weeks Assessment

Units Title of Work Weeks Assessment

Units Title of Work Weeks Assessment (end

Units Title of Work Weeks Assessment (end

HOW TO GET THE MOST FROM THIS COURSE?

In distance learning, the study units replace the conventional university

FACILITATORS/TUTORS AND TUTORIALS

There are 20 hours of tutorials provided in support of this course. As

Do not hesitate to contact your tutor by telephone, e-mail or via the

Soil microorganisms and the biochemical reactions they carryout in the

This course (SLM 505), therefore has topics on the physiology to

Unit 1 Introduction and Brief History of Soil Microbiology

UNIT 1 INTRODUCTION AND BRIEF HISTORY OF

Soil microbiology may be broadly defined as the study of

At the end of this unit, you should be able to:

• define soil microbiology

• discuss the importance of soil microbiology in agriculture.

3.0 MAIN CONTENT

3.1 Brief History of the Origin of Soil Microbiology

The origin of soil microbiology is linked with the development of

3.2 Some Important Names in Soil Microbiology and Their

(a) Waksman, S.A.:

(b) Louis Pasteur:

(c) Robert Kock:

(d) Sergei Winogradsky