The Basics of Agricultural Microbiology

The Basics of Agricultural Microbiology

The Basics of Agricultural Microbiology

Nanda Kaniyar

The Basics of Agricultural Microbiology

Nanda Kaniyar

ISBN - 9789361529535

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Preface

Just like humans, plants have recently been recognized as meta-organisms, possessing a distinct microbiome and revealing close symbiotic relationships with their associated microorganisms. The importance of microbiology has grown exponentially since the development of genomics, transcriptomics, and proteomics, making it possible to clarify microbial biogeochemical processes and their interactions with microorganisms in both health and disease. Particular attention is being paid to applied microbiology, a discipline that deals with the application of microorganisms to specific endeavors. Microorganisms, their activity and metabolites have remarkable effects on the functioning of human beings and the entire biological world, being the life-support system of the whole biosphere. Microbiology is the science exploring the interactions between micro-and macro-organisms, both in health and disease, is a branch of life sciences that has grown exponentially since the establishment of genomics, transcriptomics, and proteomics. Plants serve as hosts to numerous microorganisms. The members of these microbial communities interact with each other and with the plant, and there is increasing evidence to suggest that the microbial community may promote plant growth, improve drought tolerance, facilitate pathogen defense and even assist in environmental remediation. Therefore, it is important to understand better the mechanisms that influence the composition and structure of microbial communities and what role the host may play in the recruitment and control of its microbiome. In particular, there is a growing body of research to suggest that plant defense systems not only provide a layer of protection against pathogens but may also actively manage the composition of the overall microbiome.

This book deals with the study of microbes and the fundamental aspects of microorganisms and their relationship to agriculture. It is intended to provide an overview of the current trends into mechanisms employed by the plant host to select for and control its microbiome. It also deals with the role of keystone microbial species, phytohormones, and abiotic stress and how they relate to plant-driven dynamic microbial structuring. In addition to the microbe-rich rhizosphere, which has been studied extensively, the phyllosphere is of special interest for the study of the indoor microbiome due to its large and exposed surface area and its remarkable microbial diversity. Plants have evolved with a plethora of microorganisms having important roles for plant growth and health. A considerable amount of information is now available on the structure and dynamics of plant microbiota as well as on the functional capacities of isolated community members. Due to the interesting functional potential of plant microbiota as well as due to current challenges in crop production, there is an urgent need to bring microbial innovations into practice. Different approaches for microbiome improvement exist. The microbiome of humans and plants are currently intensively studied using the same methods and addressing similar scientific questions. The book contains an overview of the complex inter-relationship between beneficial soil microbes and crop plants and describes the potential for utilization to improve crop productivity.

Table of Contents

1 Introduction and Development of Microbiology 1

1.1 Overview Of Microbiology 2

1.1.1 Historical Background 4

1.2 Living World: Diversity 8

1.2.1 Taxonomic Categories 13

1.3 Concepts Of Spontaneous Generation 20

1.3.1 The Theory of Spontaneous Generation 21

1.3.2 Disproving Spontaneous Generation 23

1.4 Concept Of Biogenesis 25

1.4.1 Biogenesis versus Abiogenesis 28

1.4.2 Biogenesis of Ribosomes 32

1.5 Self-Assessment 32

2 Microbial Activity of Rhizosphere Microflora 33

2.1 Introduction 33

2.2 Rhizosphere Microflora: Concept 34

2.2.1 Historical Background 35

2.2.2 Microorganisms in the Rhizosphere and

Rhizosphere Effect 37

2.2.3 Factors Affecting Microbial Flora of

the Rhizosphere/Rhizosphere Effect 39

2.2.4 Alterations in Rhizosphere Microflora 42

2.2.5 Associative and Antagonistic Activities in the Rhizosphere 43

2.2.6 Rhizosphere in Relation to Plant Pathogens 45

2.3 Rhizosphere Soil Environment 47

2.3.1 Water Relations 48

2.3.2 Soil Physical Properties 49

2.3.3 Soil Chemistry 50

2.3.4 Plant-Derived Compounds 51

2.3.5 Microbial Communities 52

2.3.6 Biotic Interactions in the Rhizosphere 54

2.3.7 Mycorrhizal Fungi 57

2.3.8 Nitrogen Fixing Bacteria 59

2.4 Self-Assessment 62

3 Beneficial Microorganisms for Agriculture 63

3.1 Microorganisms In Agriculture 64

3.1.1 Agricultural Microbiology 65

3.1.2 Microorganisms In Nitrogen Cycle 66

3.1.3 Biochemical Transformations of Carbon:

The Carbon Cycle 68

3.1.4 Biochemical transformation of Sulfur: The Sulfur Cycle 69

3.1.5 Biochemical Transformation of Phosphorus Compounds 70

3.1.6 Microorganisms Involved in Bio-fertilizer 71

3.1.7 Role of Microorganisms in Industrial Processes 73

3.1.8 Importance of Microorganisms in Medicine 76

3.1.9 Plant-microbe Symbiosis 78

3.1.10 Mechanisms of Plant Growth Promotion 79

3.2 Use Of Beneficial Soil Microorganisms In Sustainable Agriculture 80

3.2.1 N2 Fixing Bacteria 81

3.2.2 Mycorrhizae and Phosphate Solubilizing Microorganisms 83

3.2.3 Plant growth-promoting rhizobacteria (PGPR) 84

3.2.4 Biological Control Organisms 84

3.2.5 Probiotics for Plants 86

3.2.6 Finding New Beneficial Inoculants 87

3.3 Utilization Of Beneficial Microorganisms In Agriculture 88

3.3.1 What Constitutes an Ideal Agricultural System? 89

3.3.2 Efficient Utilization and Recycling of Energy 89

3.3.3 Preservation of Natural Resources and the Environment 91

3.3.4 Beneficial and Effective Microorganisms for

a Sustainable Agriculture towards Agriculture without Chemicals and With Optimum Yields of High-Quality Crops 92

3.4 Controlling The Soil Microflora: Principles And Strategies 94

3.4.1 Principles of Natural Ecosystems and the Application

of Beneficial and Effective Microorganisms 95

3.4.2 Controlling the Soil Microflora for Optimum Crop Production and Protection 97

3.4.3 Application of Beneficial and Effective Microorganisms 100

3.5 Classification Of Soils Based On Their Microbiological Properties 103

3.5.1 Functions of Microorganisms: Putrefaction,

Fermentation, and Synthesis 103

3.5.2 Relationships between Putrefaction, Fermentation,

and Synthesis 105

3.5.3 Classification of Soils Based on the Functions of Microorganisms 106

3.6 Self-Assessment 110

4 Fungi as Plant Pathogens 111

4.1 introduction 111

4.2 Overview Of Plant Pathogen 113

4.2.1 The major types of Plant-Pathogenic Fungi 115

4.3 Necrotrophic Pathogens Of Immature Or Compromised Hosts 125

4.3.1 Description of Microbial Necrotrophy 126

4.3.2 Host-specific Necrotrophs 128

4.3.3 Broad-host Foliar and Soil-borne Necrotrophs 129

4.3.4 Pathogens of Fruits: the Roles of Pectic Enzymes 130

4.3.5 Host-Specialized Necrotrophic Pathogens 131

4.4 Vascular Wilt Diseases 132

4.4.1 Panama Disease: A Classic Vascular Wilt 133

4.4.2 The Disease 134

4.4.3 The Smut Fungi 135

4.5 Fungal Endophytes And Their Toxins 140

4.5.1 What are Bacterial Toxins? 142

4.5.2 Phytophthora Diseases 144

4.5.3 How to Control Phytophthora Disease 146

4.6 Self-Assessment 149

5 Position of Microorganisms in Biological World 150

5.1 Microorganisms: Definition And Types 152

5.1.1 Microorganism Definition 152

5.1.2 Types of Microorganisms 153

5.1.3 Benefits of Microorganisms for the Human Being 170

5.2 Biological Classification Of Microorganism 174

5.2.1 Kingdom Monera 178

5.2.2 Kingdom Protista 182

5.2.3 Kingdom Fungi 184

5.2.4 Kingdom Plantae 188

5.2.5 Kingdom Animalia 189

5.2.6 Viruses, Viroids and Lichens 189

5.2.7 Merits and Demerits of Five Kingdom Classification 192

5.3 Self-Assessment 193

6 Microbial Biotechnology 194

6.1 Overview Of Microbial Biotechnology 195

6.1.1 Microbes and Biotechnology 195

6.1.2 Microbial Biotechnology and its Applications in Agriculture 196

6.2 Genetic Engineering Of Microorganisms For Biotechnology 199

6.2.1 Traditional Method of Strain Improvement 200

6.2.2 Classical Genetics 200

6.2.3 Rational Selection 201

6.2.4 Cloning of the Candidate Genes 201

6.2.5 Potential Applications of Genetic Manipulation of

Micro-Organisms 203

6.3 Microbes For The Production Of Antibiotics And Enzymes 204

6.3.1 Production of Antibiotics 204

6.3.2 Production of Recombinant Microbial Enzymes 207

6.4 Microbes For Clearing Oil Spills 209

6.4.1 Environmental effects of Oil Spill 209

6.4.2 Cleanup and Recovery 210

6.4.3 Microbial bioremediation and GEMs 213

6.5 Monitoring For Microbial Pathogens And Indicators 215

6.5.1 Recreational Water Quality Criteria 216

6.5.2 Microbial Pathogens and Indicators 217

6.5.3 Sources, Fate, and Transport of Waterborne Microorganisms 223

6.5.4 Transport of Microorganisms 225

6.5.5 Monitoring Issues 228

6.6 Self-Assessment 233

7 Bacterial Morphology and Cellular Structures 234

7.1 Definition Of Bacteria 235

7.1.1 Types of Bacteria 236

7.1.2 Characteristics of Bacteria 236

7.2 Structure Of Bacteria 241

7.2.1 Cytoplasmic Membrane 245

7.2.2 Bacterial Cell Wall 255

7.2.3 Bacterial Cell Cytoplasm 257

7.2.4 Growth and Multiplication of Bacteria 271

7.3 Self-Assessment 275

Glossary 276

References 279

Index 290

Chapter 1. Introduction and Development of Microbiology

Microbiology is often incorrectly classed as the study of germs or of bacteria. While some microbiologists may specifically study viruses, also called virology, or bacteria, also called bacteriology, microbiology encompasses the whole of studying microscopic organisms. This includes the study of bacteria, protozoa, fungi, some types of algae, and often viruses.

The origins of this field can be traced to scientists positing that small useable things might affect other organisms. Anton van Leeuwenhoek was able to observe tiny bacteria in a primitive microscope in the 17th century. Many cite microbiology of medical origin as having been founded by Louis Pasteur and Robert Koch in the mid to late 19th century.

Later discoveries in the 20th century, like the discovery of viruses, proved of immense importance to medicine. Most medical professionals today credit this field with some of the most important work-related to human illness that has ever been conducted.

Medical microbiology is only one facet of the field. Other subsections of study include applications of the science to physiology, genetics, environmental studies, evolutionary biology, and pharmaceutical studies.

In each case, microbes are studied and knowledge about them contributes to these other disciplines. For example, understanding the basic make-up of microbes and how they develop and die is part of physiological microbiology. As well, evaluation of how microbes interact with each other in a complex environment enhances our understanding of our environment.

Microbiology in simple applications can also help people understand some of the basic functions of baking ingredients. For example, studies into the behavior of yeast allow people to understand how to use yeast for baking bread effectively. It also helps to explain why a loaf may fall flat.

Scientists in microbiology see the world as composed of almost uncountable numbers of tiny unseen parts that influence us in many ways. The field is constantly uncovering more that may be of benefit to all humans interacting with their environment.

Microbiology is only getting started as a science. Scientists estimate that about 99% of the microbes existing on earth have not yet been studied. This suggests that greater application of this science may further help us understand some of the mysteries of life that still daunt us.

1.1 OVERVIEW OF MICROBIOLOGY

Microbiology, a study of microorganisms, or microbes, a diverse group of generally minute, simple life-forms that include bacteria, archaea, algae, fungi, protozoa, and viruses. The field is concerned with the structure, function, and classification of such organisms and with ways of both exploiting and controlling their activities.

The 17th-century discovery of living forms existing invisible to the naked eye was a significant milestone in the history of science, for from the 13th century onward, it had been postulated that invisible entities were responsible for decay and disease. The word microbe was coined in the last quarter of the ١٩th century to describe these organisms, all of which were thought to be related. As microbiology eventually developed into a specialized science, it was found that microbes are a very large group of extremely diverse organisms.

Daily life is interwoven inextricably with microorganisms. In addition to populating both the inner and outer surfaces of the human body, microbes abound in the soil, in the seas, and in the air. Abundant, although usually unnoticed, microorganisms provide ample evidence of their presence—sometimes unfavorably, as when they cause decay of materials or spread diseases, and sometimes favorably, as when they ferment sugar to wine and beer, cause bread to rise, flavor cheeses, and produce valued products such as antibiotics and insulin. Microorganisms are of incalculable value to Earth’s ecology, disintegrating animal and plant remain and converting them to simpler substances that can be recycled in other organisms.

1.1.1 Historical Background

Microbiology essentially began with the development of the microscope. Although others may have seen microbes before him, it was Antonie van Leeuwenhoek, a Dutch draper whose hobby was lens grinding and making microscopes, who was the first to provide proper documentation of his observations. His descriptions and drawings included protozoans from the guts of animals and bacteria from teeth scrapings. His records were excellent because he produced magnifying lenses of exceptional quality. Leeuwenhoek conveyed his findings in a series of letters to the British Royal Society during the mid-1670s. Although his observations stimulated much interest, no one made a serious attempt either to repeat or to extend them. Leeuwenhoek’s animalcules, as he called them, thus remained mere oddities of nature to the scientists of his day, and enthusiasm for the study of microbes grew slowly. It was only later, during the 18th-century revival of a long-standing controversy about whether life could develop out of nonliving material, that the significance of microorganisms in the scheme of nature and in the health and welfare of humans became evident.

Spontaneous generation versus biotic generation of life

The early Greeks believed that living things could originate from nonliving matter (abiogenesis) and that the goddess Gea could create life from stones. Aristotle discarded this notion, but he still held that animals could arise spontaneously from dissimilar organisms or from the soil. His influence regarding this concept of spontaneous generation was still felt as late as the 17th century, but toward the end of that century, a chain of observations, experiments, and arguments began that eventually refuted the idea. This advance in understanding was hard-fought, involving series of events, with forces of personality and individual will often obscuring the facts.

Although Francesco Redi, an Italian physician, disproved in 1668 that higher forms of life could originate spontaneously, proponents of the concept claimed that microbes were different and did indeed arise in this way. Such illustrious names as John Needham and Lazzaro Spallanzani were adversaries in this debate during the mid-1700s. In the early half of the 1800s, Franz Schulze and Theodor Schwann were major figures in the attempt to disprove theories of abiogenesis until Louis Pasteur finally announced the results of his conclusive experiments in 1864. In a series of masterful experiments, Pasteur proved that only preexisting microbes could give rise to other microbes (biogenesis). Modern and accurate knowledge of the forms of bacteria can be attributed to German botanist Ferdinand Cohn, whose chief results were published between 1853 and 1892. Cohn’s classification of bacteria, published in 1872 and extended in 1875, dominated the study of these organisms thereafter.

Microbes and disease

Girolamo Fracastoro, an Italian scholar, advanced the notion as early as the mid-1500s that contagion is an infection that passes from one thing to another. A description of precisely what is passed along eluded discovery until the late 1800s, when the work of many scientists, Pasteur foremost among them, determined the role of bacteria in fermentation and disease. Robert Koch, a German physician, defined the procedure (Koch’s postulates) for proving that a specific organism causes a specific disease.

The foundation of microbiology was securely laid during the period from about 1880 to 1900. Students of Pasteur, Koch, and others discovered in rapid succession a host of bacteria capable of causing specific diseases (pathogens).

They also elaborated an extensive arsenal of techniques and laboratory procedures for revealing the ubiquity, diversity, and abilities of microbes.

Progress in the 20th century

All of these developments occurred in Europe. Not until the early 1900s did microbiology become established in America. Many microbiologists who worked in America at this time had studied either under Koch or at the Pasteur Institute in Paris. Once established in America, microbiology flourished, especially with regard to such related disciplines as biochemistry and genetics. In 1923 American bacteriologist David Bergey established that science’s primary reference, updated editions of which continue to be used today.

Since the 1940s, microbiology has experienced an extremely productive period during which many disease-causing microbes have been identified and methods to control them developed. Microorganisms have also been effectively utilized in the industry; their activities have been channeled to the extent that valuable products are now both vital and commonplace.

The study of microorganisms has also advanced the knowledge of all living things. Microbes are easy to work with and thus provide a simple vehicle for studying the complex processes of life; as such, they have become a powerful tool for studies in genetics and metabolism at the molecular level. This intensive probing into the functions of microbes has resulted in numerous and often unexpected dividends. Knowledge of the basic metabolism and nutritional requirements of a pathogen, for example, often leads to a means of controlling disease or infection.

1.2 LIVING WORLD: DIVERSITY

If you look around, you will see a large variety of living organisms, be it potted plants, insects, birds, pets or other animals and plants. There are also several organisms that you cannot see with your naked eye, but they are all around you. If you were to increase the area that you make observations in, the range and variety of organisms that you see would increase. Obviously, if you were to visit a dense forest, you would probably see a much greater number and kinds of living organisms in it. Each different kind of plant, animal or organism that you see represents a species. The number of species that are known and described ranges between 1.7-1.8 million. This refers to biodiversity or the number and types of organisms present on earth. We should remember here that as we explore new areas, and even old ones, new organisms are continuously being identified.

As stated earlier, there are millions of plants and animals in the world; we know the plants and animals in our own area by their local names. These local names would vary from place to place, even within a country. Probably you would recognize the confusion that would be created if we did not find ways and means to talk to each other, to refer to organisms we are talking about.

Hence, there is a need to standardize the naming of living organisms such that a particular organism is known by the same name all over the world. This process is called nomenclature. Obviously, nomenclature or naming is only possible when the organism is described correctly and we know to what organism the name is attached. This is identification.

In order to facilitate the study, a number of scientists have established procedures to assign a scientific name to each known organism. This is acceptable to biologists all over the world. For plants, scientific names are based on agreed principles and criteria, which are provided in International Code for Botanical Nomenclature (ICBN). You may ask, how are animals named? Animal taxonomists have evolved the International Code of Zoological Nomenclature (ICZN). The scientific names ensure that each organism has only one name. Description of any organism should enable the people (in any part of the world) to arrive at the same name. They also ensure that such a name has not been used for any other known organism.

Biologists follow universally accepted principles to provide scientific names to known organisms. Each name has two components – the Generic name and the specific epithet. This system of providing a name with two components is called Binomial nomenclature. This naming system given by Carolus Linnaeus is being practiced by biologists all over the world. This naming system using a two-word format was found convenient. Let us take the example of mango to understand the way of providing scientific names better. The scientific name of mango is written as Mangiferaindica. Let us see how it is a binomial name. In this name, Mangifera represents the genus, while indica is a particular species or a specific epithet. Other universal rules of nomenclature are as follows:

1. Biological names are generally in Latin and written in italics. They are Latinised or derived from Latin irrespective of their origin.

2. The first word in a biological name represents the genus, while the second component denotes the specific epithet.

3. Both the words in a biological name, when handwritten, are separately underlined or printed in italics to indicate their Latin origin.

4. The first word denoting the genus starts with a capital letter, while the specific epithet starts with a small letter. It can be illustrated with the example of Mangiferaindica.

The name of the author appears after the specific epithet, i.e., at the end of the biological name and is written in an abbreviated form, e.g., Mangiferaindica Linn. It indicates that this species was first described by Linnaeus.

Since it is nearly impossible to study all the living organisms, it is necessary to devise some means to make this possible. This process is classification. Classification is the process by which anything is grouped into convenient categories based on some easily observable characters. For example, we easily recognize groups such as plants or animals or dogs, cats or insects. The moment we use any of these terms, we associate certain characters with the organism in that group. What image do you see when you think of a dog? Obviously, each one of us will see ‘dogs’ and not ‘cats.’ Now, if we were to think of ‘Alsatians,’ we know what we are talking about. Similarly, suppose we were to say ‘mammals,’ you would, of course, think of animals with external ears and body hair. Likewise, in plants, if we try to talk of ‘Wheat,’ the picture in each of our minds will be of wheat plants, not of rice or any other plant. Hence, all these - ‘Dogs,’ ‘Cats,’ ‘Mammals,’ ‘Wheat,’ ‘Rice,’ ‘Plants,’ ‘Animals,’ etc., are convenient categories we use to study organisms. The scientific term for these categories is taxa. Here you must recognize