EM TECHNOLOGY

Ecological Concepts and Practices in Nature Farming

Editors:
Dr. Tahir Hussain: ProIessor oI Soil Science, and Director, Nature Farming Research Centre,
University oI Agrlculture, Falsalabad, Pakistan.
Mr. Ghulam Jilani: Deputy Director, Nature Farming Research Centre, University oI
Agriculture, Faisalabad, Pakistan.
Dr. Teruo Higa: ProIessor oI Horticulture, The College oI Agriculture, University oI the
Ryukyus, Okinawa, Ja pan.
Dr. Chaitat Pairintra: ProIessor oI Soil Science, Khon Kaen University, Khon Kaen, and
APNAN Coordinator, Bangkok, Thailand.
Mr. Riaz Ahmad: ScientiIic OIIicer, Nature Farming Research Centre, University oI
Agriculture, Faisalabad, Pakistan.

NFRC Publication No.3

NATURE FARMING RESEARCH CENTRE
University oI Agriculture, Faisalabad-Pakistan 1993

ACKNOWLEDGEMENTS

The authors are most grateIul to the Vice Chancellor, University oI Agriculture, Faisalabad,
Pakistan, and Mr. Yasushi Matsumoto, President oI International Nature Farming Research Center,
Atami, Japan, Ior their sincere cooperation and encouragement in the establishment oI NFRC,
Pakistan, under whose activities this book was written. The contribution oI NFRC staII especially
Mr. Sohail Ahmad, Statistician, in composing Ior this text is highly appreciated.

PREFACE

The experiments on the use oI EIIective Microorganisms (EM) Ior crop production in Pakistan
were initiated in 1990 in the Department oI Soil Science, at the University oI Agriculture,
Faisalabad. Positive eIIects oI EM were observed on a number oI crops and vegetables, thereIore,
in 1992, it was decided to extend the experimentation throughout the country. The collaborating
scientists under this programme were Ieeling lack oI technical assistance in terms oI literature Ior
understanding the mechanisms oI EM, to Iurther their research. In 1993, the establishment oI
Nature Farming Research Centre, at UAF made it possible to prepare technical documents on the
use oI EM. The Iirst attempt in this direction was, the publication oI a book entitled, "Principles oI
Nature Farming with EIIective Microorganisms" that was provided to each collaborating scientist
oI NFRC, and members oI APNAN. The present book, "EM-Technology-Ecological Concepts and
Practices in Nature Farming" has been written basically Ior the graduate students and the scientists
involved in the biotechnological research in various disciplines like agriculture, animal nutrition,
poultry husbandry, environmental pollution etc. We hope that all these personnels will be beneIited
Irom the latest ecological and biological concepts oI Iarming with microorganisms. This book has
been written with a purpose to extend the EM research Irom agriculture to other Iields also, so that
mankind can be beneIited Irom this viable, economical and environmentally saIe technology.
Clearly, it is not intended to be an advanced treatise but it is an introduction to major aspects oI
EM-Technology.

Tahir Hussain
Director,
NFRC, UAF.

Contents

Chapter Description Page
Acknowledgements 3
Preface 4
PART 1
1. Introduction 5
2. The Living World 8
3. Microbial Nutrition 48
4. Microbial Ecology 54
5. The Effective Microorganisms 62
PART 2 (in press)
6. Plant Growth with Effective Microorganisms
1) Organic Matter Decomposition
2) Soil Improvement
3) N-Iixation
4) P-Mineralization
5) K-Availability
6) Ca, Mg, S Availability
7) Micronutrients Availability
8) Plant Growth Promoting Substances and Enzymes
7. Pest Control with Effective Microorganisms
1) Insect Control
2) Disease Control
3) Weed Control
8. Animal Nutrition with Effective Microorganisms
9. Environment Protection with Effective Microorganisms
References 68
Reviews 69

Chapter 1
INTRODUCTION

The conventional agriculture based on Green Revolution Technologies has come up with the
degradation oI the natural resources and the environment. From the past decade, stagnant and even
declining trends oI crop yields have been observed mainly due to the use oI exploitive agricultural
inputs in many parts oI the world. Residues oI chemical pesticides and Iertilizers have also been
detected in the agricultural products leading to health hazards. There is a strong consensus that we
no longer can tolerate extensive soil degradation and loss oI productivity. ThereIore, Iocus must be
laid on an integrated system oI plant and animal production practices, having site-speciIic
application, that over the long-term will, satisIy human Iood and Iibre needs, enhance
environmental quality and the natural resource base, make eIIicient use oI nonrenewable resources,
use natural biological cycles and controls, improve the economic viability oI Iarming systems, and
enhance the quality oI liIe Ior Iarmers and society as a whole.
Presently, there is no Iarming system established that qualiIies Iully all these requirements.
However, agricultural scientists have recently been able to elucidate a Iew Iarming systems which
iI adopted completely, eliminate the hazards oI conventional agricultural system. These systems
either use limited chemical inputs or advocate the biotechnologies. But the dilemma is that there is
no single viable biotechnology which can substitute the chemicals completely, rather a complex set
oI technologies make the system. The Nature Farming, although, is not a new term, but with some
added dimensions in biotechnologies, it can provide the solution oI the problems oI present day
agriculture, and can also sustain the overall production.
BeIore talking about Nature Farming, let us clariIy what Nature is. Nature can be deIined as all
kinds oI existence which are leIt untouched by human beings, as all kinds oI phenomena related to
the exchange oI solar energy on land, in water, and in the atmosphere in addition to liIe on the earth,
or as the whole universe including the earth. Man is an integral part oI nature. Like the other liIe
Iorms, he draws Sustenance, Iood, water, air, space and shelter Irom nature. In order to sustain such
a large number oI living beings, nature has developed inter-dependencies and systems so that the
materials are recycled. One liIe Iorm becomes the Iood Ior the other and a Iood-chain or rather a
Iood-web is developed. Natural phenomena Iollow deIinite cycles or patterns over a time Irame.
LiIe cycles oI plant and animals Iollow a deIinite pattern. Not only living but the non living
materials oI common use the air and water also have cycles. Nature keeps its own balance
restricting the population oI a particular species to the available supply oI the necessary materials.
But giIted with mind, plan has tried to understand and then control the natural Iorces and
phenomena. He has insatiable desire Ior consumption. With control over epidemics and diseases,
the human population has been expanding by leaps and bounds. So has been his consumption
Iollowing invention oI newer uses oI natural material. This pressure has caused over exploitation oI
the natural materials, some non-renewable like minerals and mineral oil, others normally renewable
like vegetation, animals, water and air. But the pressure is too much even on these natural
resources.
The basic rule oI agriculture is to sustain human liIe with natural liIe. ThereIore, agricultural
techniques must conIorm to the evolutionary principles oI liIe, and Iollowing these principles they
must vitalize all kinds oI liIe, and secure the Ioundation oI human existence. Thus it is most
important to understand nature Irom this point oI view. Another thing which has to be realized in
understanding nature is that, when a problem occurs, nature is capable oI either eliminating
contradiction in a selI-contained way, or dissolving it by taking it in itselI in an evolutionary
Iashion, and that this leads to the stability oI nature and the principle oI evolution.
The nature Iarming is mainly based on the science oI ecology because it emphasizes the
interrelations between all living things and their environment. As this understanding takes root on
more working Iarms, it will come to be known simply as "good Iarming": that, which is based on
resource eIIicient and ecologically harmonious methods. The ecological approach makes great
economic sense as well, especially iI long-term results are considered. Many Iarmers are adopting it
because it reduces their input costs without depressing income. Small Iarmers with limited cash
Ilow must recycle out oI necessity, building proIitability Irom the ground up.
Soil management is a central Iocus oI nature Iarming, as the basis oI Iarm productivity. Skill and
planning are required to eliminate the need Ior past-acting remedies in conventional systems. Soil
quality and balance (that is, soil with proper levels oI organic matter, bacterial and biological
activity, trace elements, and other nutrients) are essential to the long-term Iuture oI agriculture.
Human and animal health is directly related to the health oI the soil. Healthy plants, animals and
humans result Irom a balanced, biological active soil. InIact it is the soil which nourishes and
provides Ior the whole oI nature, the whole oI creation depends on the soil which is the ultimate
Ioundation oI our existence.
The Iirst step towards eIIective ecological soil management is an appreciation oI the complex,
living system known as soil. And to understand soil is to be aware oI how everything aIIects and is
aIIected by it. We are all part oI the soil ecosystem. Sustainable agriculture aims Ior the protection
oI the soil's capacity to regenerate nutrients lost when crops are harvested without dependence on
"oII-Iarm" Iertilizers. The regenerative capacity thereIore depends on the numbers and kinds oI
organisms that live and die within the soil. Their Iunction is to maintain the vital biogeochemical
nutrient cycles, ensuring that the basic raw materials needed by plants are available at the right time,
and in the right Iorm and amount. The Iarm is both the product and the producer oI soil. Consider
the Iarm to be a living organism that achieves its greatest long term productivity when its natural
cycles and processes are enhanced. Short-cutting these cycles Ior short-term control or economic
gain will eventually bear out the ecological maxim, 'The creature that wins against its environment
destroys itselI.
Agro ecosystems are communities oI plants and animals and their physical and chemical
environments that have been modiIied by people to produce Iood, Iibre, Iuel and other products Ior
human consumption and processing. Agro ecology is the holistic study oI agro ecosystems,
including all environmental and human elements. It Iocuses on the Iarm, dynamics and Iunctions oI
their interrelationships and the processes in which they are involved. An area used Ior agricultural
production, e.g. a Iield, is seen as a complex system in which ecological processes Iound under
natural conditions also occur, e.g. nutrient cycling, predator/prey interactions, competition,
symbiosis and successional changes. Implicit in adapted agro ecological work is the idea that, by
understanding these ecological relationships and processes, agro ecosystems can be manipulated to
improve production and to produce more sustainability, with Iewer negative environmental or
social impacts and Iewer external inputs (Altieri, 1987).
Recent developments in microbiology and genetic engineering have revealed that most oI the
problems oI agriculture, livestock husbandry and environment can be tackled with the inclusion oI
microorganisms in the management systems. There are a number oI research Iindings available on
the beneIicial use oI microorganisms Ior soil Iertility improvement, plant and animal pest control,
animal nutrition improvement and environmental pollution control. In Japan, such a wide scope oI
biotechnology with EIIective Microorganisms (EM) was developed by Dr. Teruo Higa and his
coworkers in the last decade. The EM has been reported to be successIully used in agro Iorestry and
livestock husbandry. The EM Technology which is based on microbial ecology seems to be a viable
technology to get rid oI synthetic chemicals used in nutrition and disease control. This makes the
sustainability systems very simple and practicable by common Iarmer who can not adopt a complex
set oI technologies which are highly technical and expensive.
Chapter 2
THE LIVING WORLD

The basic use oI all scientiIic inIormation is to improve the quality oI our lives. Biology which is
the study oI living organisms is especially important Ior us because our whole existence and our
every day liIe revolves around basic biological processes. The production oI Iood and our health
are two basic aspects oI our lives without which we can not survive.
There are over two million kinds oI living organisms present on earth today. They show a lot oI
diversity in their size, shape, colour, structure and reproduction. To categorize the cellular liIe
Iorms Whittaker (1969) proposed the Iive-kingdom classiIication as in the Iollowings.
1. PLANTAE: includes all those multicellular green plants which are eukaryotes and
autrotophic.
2. ANlMALIA: are multicellular eukaryotes and heterophic in nature.
3. FUNGI: are multicellular eukaryotes and are saprophytic heterotrophs.
4. PROTISTA: includes the unicellular eukaryotes which are either autorophs or
heterotrophs.
5. MONERA: includes all the prokaryotic organisms viz. bacteria and blue-green algae,
they are either autrotrophs or heterotrophs.
However, most biologists recognize only Iour kingdoms. The Protista are distributed among the
multicellular organisms oI their kind in animals, plants or Iungi.
At the cellular level, the organisms are divided into two groups viz. Prokaryota and Eukaryota. The
diIIerence between Prokaryotic and Eukaryotic cells is given in Table 2.1.

Table 2.1: Comparison of the cell structure of Prokaryota and Euraryota.
Characteristics Prokaryote Cell Eukaryote Cell
1. Nucleus (Nuclear membrane,
chromosomes, spindle
apparatus, mitosis, meiosis)
Absent
A single molecule oI circular
DNA is present
Present

2. Cell wall Made oI amino acids, sugars
and other substances (but not
cellulose) linked to Iorm
Mucopeptide
Made oI cellulose (green
plants) or chitin (Iungi) but not
oI Mucopeptide
3. Ribosomes 70s type (ssedimentation
coeIIicient)
80s type
4. Other cell organelles
(Mitochondria, Chloroplast,
Golgi body, Endoplasmic
Reticulum, Lysosomes)
Absent Present
5. Flagella and Cilia Made oI Ilagellin molecules
twisted around each other
Show characteristic 92
Iibrillar structure


GENERAL CLASSIFICATION OF LIVING ORGANISMS
Even under a separate kingdom, the living organisms show much variation in size, shape and colour.
For a logical and meaningIul study, these organisms are arranged into groups and sub-groups. The
major basis oI classiIication is homologous structures. According to the theory oI evolution,
homologous structures indicate a common ancestry. An outline oI the classiIication oI living
organisms is given in Figure 2.1.

KINGDOM PLANTAE
In classiIication oI plants various units are used. Species represents the lowest category oI
taxonomic grouping. A species is a group oI individuals that can breed with one another in nature
and produce Iertile oIIsprings. Members oI a species resemble one another Iairly closely. Species
with many similar characteristics are grouped into the same Genus. Similar genera are grouped
together in a Family. Closely related Iamilies are grouped in Order. A group oI similar orders make
up a Class. Related classes comprise a Phylum. Finally the Phyla are grouped together in Kingdom.
The name oI the plant phyla usually ends in-phyta; the ending-eae indicates class; the ending-ales is
used Ior orders; and the ending-aceae indicates Iamily. The important phyla and groups oI land
plants are described in Figure 2.2.


Elements (Individual atoms): Inorganic and Organic molecules (non-living)
1. Viruses: Reproduce within living host cell
1.1 Procaryotic cells, no organized nucleus (Living Matter)
1.1.1 Mostly single celled
MONERA*

kingdom
Bacteria (unknown numbers)
Cyanobacteria (blue-green algae) (2500 species)
Actinomycetes
1.2 Eucaryotic cells, (Living matter) Nucleus is organized in a membrane
1.2.1 Mostly single celled
PROTISTA kingdom (25,000 species)
Protozoa, Flagellata, Amoebae, Ciliata (6000 sp.), Sporozoa
Slime molds (450 species)
1.2.2 Mostly multicellular organisms; some are single celled
FUNGI* kingdom (over 60,000 species)
Tube Iungi, rusts, molds (500 sp.)
Sac Iungi, yeasts, mildews, molds (35,000 species)
Club Iungi, rusts, mushrooms, smuts (25,000 species)
PLANTAE

kingdom
Algae, diatoms (over 20,000 sp.)
Bryophyta (mosses, others) (.250,000 species)
Trachcophyia (vascular plants) (250,000 species)
ANIMALIA

kindom
Nematoda (10,000 species)
Annelida (worms) (9,000 species)
Arthropoda (insects, centipedes) (900,000 species)
Chrordata (rodents, moles, 45,000 sp.)
Mollusca (snails, slugs, 110,000 sp.)
2. Other Substances
Note:
*Monera and Fungi kingdoms are still not universally accepted, although the two terms were
deIined in the 1930s and 1866, respectively.

Decreasing category rank: Phylum, Class, Order, Family, Genus.

Decreasing category rank: Division, Class, Subclass, Order, Family, Genus, Species, Variety.

Decreasing category rank: Phylum, Subphylum, Superclass, Class, Order, Family, Genus,
Species, Subspecies.
(Source: Raymond W.Miller, Utah State University, Irom data by Edward W.Wilson et al, LiIe oI
Earth, Sinauer Associates, Inc.,1974, StamIord, Conn.,p p.1033)

Figure 2.1: General classlfication of living organisms with emphasis on the organisms most
active in soils. Most subkingdoms listed are common names within the Iive kingdoms, but are not
phyla names in most instances.


PLANTAE
1. Bryophyta (non vascular) e.g. Liverworts and Mosses
2. Tracheophyta (vascular)
2.1 Lower vascular plants or Pteridophytes (Reproduce through spores) e.g. Rhynia,
Psilotum, Club Mosses, Horsetails, and Ferns
2.2 Higher Vascular plants (Reproduce through seeds)
2.2.1 Gymnosperms (Produce naked seeds) e.g. ConiIers inclusing Pinus (Pines, chir, kail),
Abies (Iirs) and Cedrus (cedars). They are tall evergreen trees.
2.2.2 Angiosperms (Seeds enclosed in .a Iruit) e.g. rose, mustard, rice, wheat and maize
etc. They are the Ilowering plants.
Brassicaceae (Mustard Family): 350 genera, and 3,000 species)
Solanaceae (Potato Family): 90 genera, and 2,000 species
Leguminosae (Pea Family): 600 genera, and 15,000 species
Gramineae (Grass Family): 600 genera, and l0,000 species

Figure 2.2: The schematic representation of the important phyla in the Kingdom Plantae.


Algae
The study oI algae is called Phycology. The group algae includes aquatic photosynthesizing
organisms with a thallus plant body. ThereIore, algae are eukaryotic chlorophyllous thallophytes.
About 23,000 species oI algae have been described. They are divided into many groups on the basis
oI their pigments and other Ieatures. Important groups oI algae are Chlorophyta (green algae),
Cynophyta (blue-green algae though it is now included in teh kingdom Monera as it is prokaryotic),
Bacillariophyta or Christophyta (diatoms), Rhodophyta (red algae). Chlamvdomonas is example oI
unicellular, whereas Stigeoclonium and Ulva are multicellular algae.
Algae develop best in moist Iertile soils. Algae are not important as decomposers oI organic matter
but are producers oI new photosynthetic growth. The green algae are most evidept in nonIlooded
soils, especially iI the pH is low. The mass oI live algae in soils may range Irom 50-600 kg per
hectare Iurrow slice. Unusual symbiotic algae (either blue green algae or green algae) associate
with one oI several Iungi in Iorms called Lichins. The algae Iix dinitrogen, and the Iungi attack to a
surIace and Iorm a protective mat that tenaciously holds water and supplies other nutrients to the
algae. Lichens grow extremely slowly (1-30 mm per year), they help to weather rock surIacbs, and
they can grow on bark and other surIaces. The major groups oI the algae alongwith important
genera are given in the Iollowing scheme.

Algae
Chlorophyta (green algae) unicellular but Iilamentous
Ankistrodesmus
Characium
Chlamydomonas
Chlorella
Chlorococcum
Dactylococcus
Hormidium
Protococcus
Protosiphon
Scenedesmus
Spongiochloris
Stichococcus
Ulothrix
Bacillario phyta (diatoms) unicellular/colonial surrounded by siliciIied outer layer.
Achnanthes
Cymbella
Fragilaria
Hantzchia
Navicula
Nitzchia
Piunularia
Surirella
Synedra
Xantho phyta (yellow-green algae)
Botrydiopsis
Bumelleria
Bumelleriopsis
Heterococcus
Heterothrix
Euglenophyta (Chlorophyll-bearing unicellular Ilagelates)
Euglena
Cyanophyta (blue-green algae)
Now included in kingdom Monera.

Figure 2.3: Schematic description of the important major groups of algae.


KINGDOM ANIMALIA
On the basis oI their structure, physiology, reproduction, development, biochemical processes,
inheritance and evolutionary history, various kinds oI animals are arranged into major groups
known as phyla and then each phylum is systematically divided towards the lower grade in the
manner as Kingdom-Phylum-Class-Order-Family-Genus-Species. The schematic classiIication oI
the major groups is given in Figure 2.4.
Organisms belonging to the Kingdom Animalia are heterotrphic-obtain their cnergy and carbon
Irom the breakdown oI organic materials and are unable to manuIacture their Iood Irom inorganic
ingredients as the plants can do it. There are a number oI macro as well as micro animals that aIIect
the growth oI plants and most oI them are soil inhabiting.

ANIMALIA
1. Protozoa (Unicellular) 45,000 species
e.g.Amoeba, Euglena, Paramecium, Plasmodiun, Trypanosoma, Vorticella.
2. PoriIela (Simplest multicellular)
e.g. Sponge.
3. Coelenterata (Two-layered)
e.g. Hydra, Jelly Iish, Sea anemone.
4. Platyhelminthes (Three layered Flatworms)
e.g. Planaria, Liver-Iluke, Tape-worm (parasites)
5. Nematoda (Round and cylinderical body pointed at both ends-Round worms)
e.g. Ascaris.
6. Annelida (Segmented worms)
e.g. Leech, Earth worm.
7. Arthropoda (Animals with jointed legs)
7.1 Crustaceans (Mostly aquatic)
e.g. Water Ilea, Prawn, Labsters, Crabs etc.
7.2 Insects (Have 3 pairs oI legs).
7.3 Arachinids
e.g. Spiders, Scorpions, Ticks, and Mites.
7.4 Myriapods
e.g. Centipedes, and Millipedes.
8. Mollusca (Unsegmented body having head, Ioot and a dorsal visceral region)
8.1 Bivalves
e.g. Sea mussels
8.2 Gastropods
e.g. Snails.
8.3 Cephalopods
e.g. Squids, Octopases
9. Echinodrmata (Spiny skinned animals) Exclusively marine
e.g. Star-Iish, Brittle-star, Sea-unchin, Sea-cucumber.
10. Chordata (Possess Notochard, Gill slits, and Nervous system).
10.1 Vertebrata
10.1.1 Pisces (Aquatic)
e.g. Fishes.
10.1.2 Tetrapoda (Terrestrial)
10.1.3 Amphibra
e.g. Frogs and Toods.
10.1.4 Reptilia
e.g. Snake, Tortoise, Lizard, Alligator.
10.1.5 Aves (Birds)
10.1.6 Mammalia
10.1.6.1 Prototheria (Egg-laying)
10.1.6.2 Metatheria (Pouched)
10.1.6.3 Eutheria (Placental)
10.2 Protochordates (Lower chordata)
e.g. Amphioxus.

Figure 2.4: The schematic representation of the Kingdom Animalia.

Large burrowing animals e.g. moles, prairie, dogs, gophers, mice, shrews, rabbits, badgers,
woodchucks, armaldillos and chipmunks etc. aerate the soil and alter its Iertnity and structure, but
they eat and destroy vegetation also, which makes them more detrimental than beneIicial.
Earthworms are probably the most important soil macroanimals much appreciated by gardeners,
agronomists and Iishermen. They belong to phylum Annelida and more than 1800 species are
known worldwide. Earthworms do not eat living vegetation but only dead organic matter. The
ingested organic matter and Iine textured soil are excreted as small granular aggregates, which
resist rupture by rain drop impact and provide abundant and readily available plant nutrients.
Earthworms aerate and stir the soil, which allows better water inIiltration and easier root
penetration. The enemies oI earthworms are heavy Iarm machinery; sandy, salty, arid, acid, cold or
hot, bare or barren soils; mice, moles, mites, millipedes; and strong insecticides.
Arthropods which are joint-Iooted invertebrate organisms and include mites, millipedes, centipedes,
and insects such as spring-tails, proturans, diplurans, and the larvae oI beetles, Ilies, ants and
termites. They Ieed mostly on decaying vegetation and help to aerate the soil with their burrows;
however many species also can be pests because they are phytophagous (eat the plants). Termites
(white ants) are major contributors to the breakdown oI organic material in or at the surIace oI soils.
There are about 2,000 species oI termites. In building their honeycombed mounds, termites
transport soil Irom lower layers to and above the surIace soil level, thereby bringing about
extensive mixing oI soil materials and the plant residues they use as Iood. Ants, although have less
widespread inIluence on soil properties than earthworms and termites, locally they have notable
eIIects. For example, some ant species are known Ior their exceptional ability to break down woody
materials. There is considerable turnover in the soil associated with the mounds and nests oI ants
because sub-soil is brought to the surIace. Gastropods (belly-Iooted organisms) e.g. slugs and snails
Ieed on decaying vegetation but will eat and damage living plants.
OI the abundant microanimals in soils, three groups are oI some imporatance viz. nematodes,
protozoa, and rotiIers. Nematodes (threadworms or eelworms) are microscopic, unsegmented,
threadlike worms, and Iound in almost all soils. The most numerous nematodes are omnivorous
which live mainly on decaying organic matter (saprophytes), or are predatory on soil bacteria, Iungi,
algae, protozoa and even other nematodes. But some nematodes, especially those oI the genus
Heterodera are Parasitic which can inIest the roots oI all plant species causing the conspicuous
knots that give visible prooI oI their presence. Protozoa are probably the simplest Iorm oI animal
liIe and are the most varied and numerous oI microanimals in soils. Although unicellular, they are
considerably larger than bacteria, having a diameter range Irom less than 5 to greater than 100 m,
and are oI a distinctly more complex organization. Soil protozoa include amoeba, ciliates and
Ilagellates. In soil, more than 250 species are known and they thrive best in moist well-drained soils
and are most numerous in surIace horizons. Some protozoa are predators on soil bacteria and other
microIlora, especially in the rhizosphere. A considerable number oI serious animal and human
diseases are attributed to protozoan inIections. Prozoans do not contribute much in organic matter
decomposition and nutrient release as they are not suIIiciently abundant in soils to be a major Iactor.
RotiIers thrive under moist conditions, and about 100 species have been identiIied in soil. Their
activities in soil are unknown, however, they are conIined to wet areas oI mineral soils and peat
bogs.

KINGDOM FUN1I (Mycota)
The study oI Iungi is called Mycology. Fungi are eukaryotic microorganisms which resemble plants
in that they have cell wall, but they lack chlorophyll. They live on dead or living plant or animal
tissue. Fungi are a curious assortment oI unicellular organisms yeasts, multicellular Iilamentous
molds, mildews, smuts, rusts and the well known mushrooms. The cell wall oI Iungi is not like that
oI plants. It is made up oI chitin and not cellulose (except in Oomycetes). Their storage product
also diIIers Irom plants in not being starch but oil and glycogen which occur in animals. There are
about 80,000 species oI Iungi, and only in soil over 690 species have been identiIied, representing
170 genera. The body oI Iilamentous Iungi is composed oI thread like structures called hyphae, and
the mass oI hyphae is called mycellium. The hyphae contain nuclei and cytoplasm and are either
divided into cells by cross walls (septate) or lack cross walls (non-septate). Molds on bread, on
cheeses, on many rotting Ioods, and in Iorest litter exhibit mycelia. Fungi are vigorous
decomposers oI organic matter and readily attack cellulose (cellulolytic Iungi), cutin (cutinolytic
Iungi), lignin (lignin decomposing Iungi), dung oI herbivores (coprophilous Iungi) and dead
remains oI animals (Keratinaceous Iungi) even in quite acidic conditions, where bacteria and
actinomycetes oIIer only mild competition. Fungi also compete with economic plants Ior nutrients
released Irom organic residue decomposition, particularly nitrogen, phosphorus and sulIur. Fungi
also secrete substances that aid in the Iormation oI water-stable soil aggregates.
The taxonomic grouping oI the Iungi in a descending order with their end names in parenthesis is
as: Kingdom-Division (mycota) - Sub division (mycotina) - Class (mycetes) - Sub class
(mycetidae) - Order (ales) - Family (aceae). The kingdom is divided into two divisions viz.
Myxomycota (Ior plasmodial Iorms) and Eumycota (Ior non plasmodial, usually Iilamentous Iorms
with cell wall). The detailed classiIication oI Iungi upto class level is given in Figure 2.5. The
classiIication Iollowed here is based on that proposed by Ainsworth (1966) and characterized by
Lynch and Poole (1979).
The classiIication upto class-level has no signiIicance rather a more detailed classiIication upto
species level would be needed iI a particular purpose is to be met Irom the Iungi. Although it will
be beyond the scope oI this text to give a Iull classiIication, however, the economically important
groups/species oI Iungi riave been enlisted in the Iollowing Iigures.

KINGDOM MYCOTA (Fungi) (2 divisions)
1. Eumycota (5 sub-divitions)
1.1 Mastigomycotina (motile stages in their liIe cycle)
1.1.1 Chytridiomycetes
(aquatic living on detritus such as Iallen leaves, chitinous walls; zoospores have one
posterior whiplash Ilagellum. Some species parasite on protozoa, algae particularly diatoms
or blue green algae).
1.1.2 Hyphochyiridiomycetes
(marine or Ireshwater; unicellular, zoospores have a single tinsel Ilagellum).
1.1.3 Oomycetes
(aquatic or parasitic on plants and Iish, sharing with green algae, such biochemical
characters as a cellulosic wall and phyiosterols; zoospores have two Ilagella, the leading
'tinsel' Ilagellum decorated with rows oI Iibrils, and the trailing 'whiplash' Ilagellum).
1.1.4 Plasmodiophoromycetes
(plant parasitic amoeboid cells: plasmodiophora brassicae is the cause oI club-root oI
cruciIerous plants).
1.2. Zygomycotina
(typically ephemeral saprophytic opportunists, spreading quickly through habitats rich in
simple carbohydrates or starch, and readily sporulating; sporangiospores Iormed in large
numbers, readily dispersed by air current or water droplets; mycelium coenocyiic, i.e. without
regular cross-walls. A Iew species are pamsitic on other Iungi, animals or plants.
1.2.1 Zygomycetes
1.2.2 Trichomycetes
1.3. Aschomycotina
(and the majority oI the 'Iungi imperIecti'). |septate hyphae; saprophytes and parasites. Many
cause the soIt rots oI stored products. The hemiascomycetes (with their ascospores Iormed in a
naked ascus, and not in a structured Iruiting body) include the Iamiliar yeasts, Saccharomyces
species|
1.3.1 Hemiascomycetes
1.3.2 Loculoascomycetes
1.3.3 Plectomycetes
1.3.4 Laboulbeniomycetes
1.3.5 Pyrenomycetes
1.3.6 Discomycetes
1.4. Basidiomycotina
(mushrooms and toadstools, as ephemeral Iruiting bodies, producing large numbers oI
basidiospores, Irom a parent mycelium oI a continuum oI interconnecting hyphae that can be
very large and old, Ior example as old as the tree in the case oI a mycorrhizal Iungus, and
sometimes many hundreds oI years old in the case oI Iairy rings, many are important wood
rotters. giving rise to brown rots and white rots. Heterobasidiomycetes, with septate basidia,
include the smuts and rusts, important plant parasites).
1.4.1 Teliomycetes
1.4.2 Hymenomycetes
1.4.3 Gasteromycetes
1.5. Deuteromycotina
(deuteromycetes, Iungi imperIecti) |septate mycelium; reproduce only by asexual methods;
lack sexual reproduction or the perIect stage and are, thereIore, "Fungi ImperIecti". Conidia
resemble the conidia oI Ascomycotina. In the absence oI sexual reproduction the genetic
variations are brought about by mutation and heterokaryosis (occurance oI diIIerent types oI
nuclei in the same cyioplasm), and rarely by parasexual phenomenan (a noval type oI sexual
reproduction)|.
1.5.1 Blastomycetes
1.5.2 Hyphomycetes
1.5.3 Coelomycetes.
2 Myxomycota (slime molds) 4 classes
2.1 Acrasiomycetes-Cellular slime moulds
(Also Iorm spores on a Iruiting body, but with vegetative phase oI individual amoebae which
engulI bacteria or other Iood; probably quite common in soil).
2.2 Hydromyxomycetes
2.3 Myxomycetes-True slime moulds
(vegetative phase oI growth as a plasmodium, see as a thin Iilm oI protoplasm on rotting wood,
perhaps several centimeter across, which is one multinucleate coenocyie; engulIing bacteria,
or digesting substrates with extra-cellular enzymes; when starved it Iorms spores, oIten an
intricately sculptured Iruiting body).
2.4 Plasmodiophoromycetes
(see under Eumycota)

Figure 2.5: The schematic division of Kingdom Mycota upto class-level, alongwith some
prominant characteristics.



1.1 Mastigomycotina
1.1.1 Chyiridiomycetes
1.1.1.1 Chytridiales
(True mycelium absent; rhyzomycelium present in some species)
1.1.1.1.1 Olpidiaceae
(Thallus is endobiotic i.e. remains inside host cell)
1.1.1.1.1.1 Olpidium -include 130 species.
(Vector oI viruses causing plant diseases; parasitize algae and roots oI higher plants)
Olpidium brassicae
(inIects roots oI cabbage and other spp. oI Brassica)
Olpidium viciae (inIects leaves and stems iI Vicia umjuga)
1.1.1.2 Blastocladiales
1.1.1.3 Monoblepharidales
1.1.2 Plasmodiophoromycetes
Plasmodiophorales
Plasmodiophoraceae
(obligate parasites oI higher plants, algae and Iungi)
Plasmodiophora
P. brassicae
(causes the club-root desease oI cruciIers especially the mustard and cabbage)
1.1.3 Oomycetes
1.1.3.1 Saprolegniales (water mold)
1.1.3.1.1 Saprolegniacea
Saprolegnia-primary sugar Iungi (aquatic submerged Iungus, occur Irequently
on plant and animal debris; Iail to decmpose cellulose)
Achlya (Iound in ponds and soil)
1.1.3.1.2 Thraustochytriaceae
1.1.3.1.3 Ectrogellaceae
1.1.3.1.4 Haliphthoracea
1.1.3.1.5 Leptolegniellaceae
1.1.3.2 Leptomitales
1.1.3.3 Lagenidiales
1.1.3.4 Peronosporaies
1.1.3.4.1 Pithiaceae
1.1.3.4.1.1 Pithium
92 species (attakcs several crop plants and causes root-rot and damping oII oI
seedlings)
P. debaryanum (Damping oII oI tobacco and chillies)
P. aphanidermatum (SoIt rot oI papaya. damping oII oI potato)
P. graminicolum (Rhizome and root-rot oI turmeric)
P. myriotylum (Foot rot oI ginger)
1.1.3.4.1.2 Phyiophthra (caused Irish Potato Famine)
P. inIestans (Late blight oI potato)
P. colocasiae (Colocasia blight)
P. Parasitica var. sesami (LeaI blight oI Sesamum)
P. Palmivora (Bud rot oI toddy palm and coconut palm)
1.1.3.4.2 Albuginaceae
AlbugoCystopus
25 species (Obligate parasites oI higher plants, causing white blisters on the Ioliage)
A. candida (inIects members oI CruciIerae like brassica, cabbage)
A. Ipomae-panduranae (inIects plants oI Convolvulaceae)
A. bliti (inIects Amaran- taceae)
A. tragapogonis (inIects Compositae)
A. occidentalis (inIects Spinach)
A. portulaceae (inIects Portulaca)
1.1.3.4.3 Peronosporaceae
(Causes downy mildew diseases oI several crops)
Peronospora
Bremia
Basidiospora
Sclerospora
Plasmopara
Pseudoperonospora
Bremiella

Figure 2.6: Schematic description of the important fungi belonging to sub-division of
Mastigomycotina.

1.2 Zygomycotina
1.2.1 Zygomycetes 3 orders
1.2.1.1 Mucorales
(ChieIly saprophytic) Pin molds or sugar Iungi 14 Iamilies
1.2.1.1.1 Mucuraceae
Mucor
42 species (essentially saprophytes used in Iermentation oI starch into glucose which
is then acted upon by yeast. Yeast does not produce amylase hence can not degrade
starch)
Rhizopus
(used in Iermentation oI starch to sugars also attacks as parasite on apples especially
during storage causing soIt rot)
1.2.1.1.2 Pilobolaceae
Pilobolus shot gun Iungus or the hat-thrower (it is coprophilous i.e. Iound on dung
oI herbivore animals)
1.2.1.2 Entomophthorales
(ChieIly parasitic on insects)
Entomophthoraceae 6 genera
Entomophthora
100 species (attacks several insects)
E. muscae
(attacks house-Iiy and causes Ily cholera)
R. stoloniIer R. nigricans
(produces Iumaric acid and lactic acid)
R. oryzae
(produces alcohol)
R. sinensis
(produces lacticacid)
R. nodosus
(produces lactic acid)
1.2.1.3 Zoopagales

Figure 2.7: Schematic description of the important fungi belonging to sub-division of
Zygomycotina.

1.3 Ascomycotina 6 classes
1.3.1 Hemiascomycetes
1.3.1.1 Endomycetales
Ascoidaceae
Sacchromycetaceae
Saccharomyces (Yeast)
S. cerevisiae (Brewer's and Baker's yeast) (Known as sugar Iungi, under aerated
condition Ierments sugar into CO
2
and H
2
O, under anaerobic condition
produces ethyl alcohol and CO
2
Irom sugar. yeasts are the richest source oI
vitamin B-complex).
Endomycetaceae
Spermophthoraceae
1.3.1.2 Taphrinales
1.3.2 Loculoascomycetes
1.3.3 Laboulbeniomycetes
1.3.4 Plectomycetes
1.3.4.1 Eurotiales
Eurotiaceae
Aspergillus
(hydrolyse starch into glucose in alcoholic Iermentation)
A. niger (black mould; produces citric acid, gluconic and itaconic acids)
A. Ilavus (green mold; produces toxin AIlatoxins that kills poultry)
A. glaucus (This species is most xerophytic)
A. halophilicus (as above)
A. restrictus (as above)
A. ochraceus (Yellow mold)
A. tamari (brown mold)
A. candidus (white mold)
Penicillium
P. notatus (Produces Penicilin discovered by Alexander Fleming)
P. chryrsogenum (Produces Penicilin commercially)
P. griseoIulvum (Produces antibiotic GriseoIulvin)
P. roqueIort (used Ior cheese production)
P. camemberti (used Ior cheese production)
P. italicum (blue mold oI citrus Iruits)
P. digitatum (green mold oI citrus Iruits)
P. expansum (rot oI apples)
1.3.4.2 Oxygenales
1.3.4.3 Microascales
1.3.5 Pyrenomycetes 4 orders
1.3.5.1 Erysiphales (ectoparasites on higher plants)
1.3.5.1.1 Erysiphaceae (Powdery Mildews-obligate parasites oI higher plants)
Sphaerotheca
Podosphaera
Erysiphae
Phyllactinia
Microsphaera
Uncinula
Levillula
Acrosporium
1.3.5.1.2 Perisporiaceae
1.3.5.2 Meliolales
1.3.5.3 Coronophorales
1.3.5.4 Sphaeriales
Melanosporaceae
Chaetomium (cellulose degrading)
C. globosum (cellulolytic and coprophylous)
Diaporthaceae
Xylariaceae
Clavicipitaceae
Hypocreaceae
1.3.6 Discomycetes
1.3.6.1 Medeolariales
1.3.6.2 Cyttariales
1.3.6.3 Tuberales
1.3.6.4 Pezizales
Pezizineae
Peziziaceae
Peziza (Saprophytes on wood, manure and soils rich in organic matter)
P. vesicular (pale coloured)
P. aurantia (brillient orange coloured)
Sarcoscyphineae
Morchella (Morels or sponge Mushrooms)
M. conica (conical morel)
M. delicosa (delicious morel)
M. hybrida (hybrid morel)
M. esculenta (common morel)
1.3.6.5 Phacidiales
1.3.6.6 Ostropales
1.3.6.7 Helotiales

Figure 2.8: Schematic description of the important fungi belonging to sub-division
Mastigomycotina.

1.4 Basidiomycotina 3 classes
1.4.1 Teliomycetes
1.4.1.1 Uredinales
(Rust Iungi which total about 100 genera and 4000 species; all are obligate parasites oI
angiosperms, gymnosperms and Ierns)
1.4.1.1.1 Pucciniaceae
1.4.1.1.1.1 Puccina
P. graminis
P. graminis tritici (black rust oI wheat)
P. g. avenae (inIects oats)
P. g. hordei (inIects barley)
P. g. secalis (inIects rye)
|Even these sub-species consist oI physiological races which grow only on a
particular veriety oI the host. These races are designated by numhers. e.g., P.
graminis tritici 138|.
P. malvacearum (hollyhock rust)
P. covonata (crown rust)
P. antirrhini (snapdragon rust)
1.4.1.1.1.2 Melam psoraceae
1.4.1.1.1.3 Coleosporiaceae
1.4.1.2 Ustilaginales
(Smut Iungi)
1.4.1.2.1 Ustilaginaceae
Ustilago (all species live as parasites except U. maydis which grows on manure heaps)
U tritici (loose smut oI wheat)
U. nuda (loose smut oI barley)
U. avenae (loose smut oI oats)
U. maydis (smut oI maize)
U. scitaminea (smut oI sugarcane)
U. occidentalis (smut oI cyanodon)
1.4.1.2.2 Tilletiaceae
1.4.1.2.3 Graphiolaceae
1.4.2 Hymenomycetes 2 sub-classes
1.4.2.1 Phragmobasidiomycetidae
1.4.2.2 Holobasidiomycetidae
1.4.2.2.1 Agaricales (Mushrooms and toadstools)
Agricaceae
Agricus
A.campestris:Psalliota campestris or A. bisporus (industrial name) (Extensively
cultivated mushroom)
Boleus
Lepiota
Morchella
Volvariella
V.volvacea
Amanita-toadstool (Poisonous mostly)
A. phalloides ('death cap' - very poisonous)
A. muscaria ('Ily agaric- poisonous)
A. pantherina ('panther cap' -poisnous)
A. citrina ('Ialse death cap' -harmless)
A. rubescenes ('blusher' -edible)
1.4.2.2.2 Aphyllophorales
Polyporaceae (lignicolous-lignin decomposer, humicolous and sometimes parasitic)
Polyporus (Wood-rotting Iungi)
P. sulphurens (wood-rot oI oak)
P. squamosus (heart-rot oI trees)
P. betulinus (heart rot oI birch trees)
P. schweinitzii (Butt-end rot)
1.4.3 Gasteromycetes 9 orders
Lycoperdales (PuII balls and earth stars)
Lycoperdaceae
Lycoperdon (Common PuII Ball)
Geastraceae
Geastrum (The Earth Star)

Figure 2.9: Schematic description of the important fungi belonging to sub-division
Basidiomycotina.

1.5 Deuteromycotina (Fungi Imperfecti)
1.5.1 Blastomycetes
1.5.2 Hypomycetes
1.5.2.1 Alternaria
Several saprophytic and parasitic species
tenuis
solani (early blight oI potato)
1.5.2.2 Piricularia
P. oryzae (blast disease l oI rice)
1.5.2.3 Helminthosporium
H. oryzae (leaI-spot oI rice)
H. maydis (leaI-spot oI maize)
H. victoriae (victoria blight oI oats)
1.5.2.4 Fusarium
F. oxysporum (root rot and l wilt diseases)
1.5.3 Coelomycetes
1.5.3.1 Melanconiales
Melanconiaceae
Majority is parasitic causing leaI spots
1.5.3.1.1 Pestalotiopsis
P. theae (grey blight oI tea)
P. paucista (leaI spot oI litchi)
P. manglIerae (leaI spotoI mango)
1.5.3.1.2 Colletotrichum
C. Ialcatum (red rot oI sugarcane)
C. lindernuthianum (anthracnose oI bean)
C. cerchorum (anthracnose oI jute)
1.5.3.1.3 Gloeosporium
C. corchorum (anthracnose oI jute)
1.5.3.2 Sphaeropsidales
Phoma (grows on stem)
Phyllosticta (grows on leaves)
Diplodia
Septoria
Macrophomina (grows on stem)

Figure 2.10: Schematic description of the important fungi belonging to sub-division
Deuteromycotina.

KINGDOM PROTISTA
Some organisms show characteristics oI both plants and animals. ThereIore, the organisms which
are motile (animal character) and green (plant character) are put in a separate phylum Protista. By
deIinition, this phylum includes the unicellular or colonial-unicellular organisms (but simple
multinucleate organisms or stages oI liIe cycles occur in a number oI groups), with eukaryotic cells
like protozoa (Ilagellata, amoebae, ciliata and sporozoa) and slime molds. However, most biologists
still do not recognize the Protista phylum, thereIore, the protista are distributed among the
multicellular organisms oI their kind in animals, plants or Iungi. Many species oI Protista are one
celled. Some are colonial or even Iilamentous. They make their own Iood or take it Irom an outside
source, viz. photosynthesis, absorption, ingestion, and combinations oI these. Reproductive cycles
varied, but typically including both asexual division at the haploid level and true sexual processes
with karyogamy and meiosis. Motile by advanced Ilagella or other means, or nonmotile. In the
Iollowings are given the phyla oI the kingdom Protista.

1. Euglenophyta - Euglenoid organisms
2. Chrysophyta - Golden algae
3. Phyrrophyta - DinoIlagellates and cryptomonads
4. Hyphochytridiomycota - Hyphochytrids
5. Plasmodiophoromycota - Plasmodiophores
6. Sporozoa - Sporozoans
7. Cnidosporidia - Cnidosporidians
8. Zoomastigina - Animal Ilagellates
9. Sarcodina - Rhizopods
10. Ciliophora - Ciliates and suctorians

KINGDOM MONERA
The kingdom Monera includes the microscopic prokaryotic mostly unicellular or colonial
unicellular organisms. The major groups in this kingdom are bacteria, cynobacteria (blue-green
algae) and actinomycetes. Most oI the bacteria and actinomycetes decompose organic matter,
although actinomycetes are not as eIIective as bacteria or Iungi. Actinomycetes are the source oI
numerous beneIicial antibiotics, but they can also produce musty taste and odours to waters. In
Monera, the predominant nutritive mode absorption, but some groups are photosynthetic or
chemosynthetic. Reproduction primarily asexual by Iission or budding; protosexual phenomena
also occur. Motile by simple Ilagella or gliding, or nonmotile. The detailed classiIication oI the
major groups oI kingdom Monera is as under in the Figure 2.11..

MONERA
1. Myxomonera (without Ilagella, motility iI present by gliding)
1.1 Cynophyta (blue-green algae)
1.2 Myxobacteriae (gliding bacteria)
2 Mastigomonera (Motile by simple Ilagella, and related nonmotile Iorms)
2.1 Eubacteriae (true bacteria)
2.2 Actinomycota (mycelial bacteria)
2.3 Spirochaetae (Spirochaetes)

Figure 2.11: Schematic description of the major groups in the kingdom Monera.

In a general classiIication oI the prokaryotic microorganisms, three classes have been deIined in the
old system in which bacteria were put under the Division oI Protophyta oI the Plantae Kingdom.
This scheme as proposed in Bergey's Manual oI Determinative Bateriology (1957) is in the
Iollowings:

PROTOPHATA (primitive plants)
1. Schizophyceae (blue-green algae)
2. Microtatobiotes (includes the smallest oI the living things e.g. Rickettsia, Virus)
3. Scizomycetes (bacteria and actinomycetes)

The Blue Green Algae (BGA) possess the photosynthetic pigment phycocyanin in addition to
chlorophyll. The BGA diIIer structurally Irom all other types oI Thallophyta as the BGA possess
prokaryotic cell. Since the blue-green algae resemble the bacteria, both are commonly classed in
the same kingdom Monera in the modern classiIication. Cynobacteria (BGA) are the simplest oI the
oxygen producing photosynthetic organisms. Blue green algae possess chlorophyll a and phycobilin
pigment. They can be Iound in almost any damp environment - in saltwater and Ireshwater, in
moist soil, on damp rocks and tree trunks. They can grow even in hot springs with temperature upto
85C. Some oI them are symbionts and others are epiphytes. Many species are unicellular and
solitary while some others Iorm round colonies consisting oI several to many cells, and still others
are Iilamentous. Filaments are composed oI cells attached end to end, like beads on a string. Their
cell wall contains muramic acid not Iound in eukaryotic cell wall. The outside oI cell wall is oIten
surrounded by a protective jelly like layer or mucilaginous sheath. About one-third species oI all
blue green algae are able to Iix atmospheric nitrogen. In most cases N-Iixation occurs in specialized
cells called Heterocysts which are enlarged cells with a unique thick envelop. The N-Iixing BGA
include Nostoc and Anabaena. Reproduction in BGA is purely asexual through harmogonia,
akinete or spores (not common). The most common genera in paddy Ilelds responsible Ior
N-Iixation are, Anabaena, Anabaenopsis, Aulosira, Cvlindrospermum, Nostoc, Calothrix,
Scvtonema, Tolvpothrix, Fischerella, Haplospiphon, Masligocladus, Stigonema, Westiella,
Westiellopsis, Campvlonema and Michrochaete. Besides N-Iixation, the BGA excrete vitamin B
12

auxins ascorbic acid which may also contribute to plant growth.

Actinomycetes resemble molds in that they are Iilamentous, oIten proIusely branched. Their
mycelial threads are smaller, however, than those oI Iungi. Actinomycetes are similar to bacteria in
that they are unicellular and oI about the same diameter. When the mycelia break into short
Iragments (spores), they closely resemble bacteria. Actinomycetes develop best in moist, well
aerated soil, however, in times oI drought, they remain active to a degree not usually exhibited by
either bacteria or molds. Their optimum development occurs at pH values between 6.0-7.5. The
number oI actinomycetes in soil exceeds those oI all organisms except bacteria. These are oI
special importance in the decomposition oI organic matter, particularly cellulose chitin,
phospholipids, and other resistant molecules. Like Iungi, actinomycetes aid in the development oI
water-stable soil structure by secreting non-water-soluble gummy substances. They produce many
useIul antibiotics, and about 500 antibiotics have been isolated Irom actinomycetes, the most
common oI which are streptomycin, aureomycin, terramycin and neomycin. It has also been Iound
that actinomycetes Iorm symbiotic N-Iixing relationships with a diverse selection oI plants, e.g.
with boysenberry, soapberry, bayberry, coIIeeberry, buIIaloberry, alders, sweet Iern, sweet gale,
bitterbrush, mountain mohaganies, Australian pine, European autumn, New Jersey tea, Russian
olive and Ilooded rice. Symbiotic actinomycetes inIect atleast seven diIIerent botanical Iamilies
whereas Rhizobia bacteria inIect only the Iamily Leguminosae. N-Iixation in red alder has been
measured as high as 168 kg per hectare per year. Actinomycetes are well known Ior the
transIormations at high temperature particularly in the rotting and heating oI green manures, hay,
compost piles, and animal manures. Here, Thermoactinomycetes, certain streptomycetes and
species oI spore-Iorming bacteria have the competitive advantage. They can also be the cause oI
certain soil-borne diseases oI plants e.g. potatoscab by Streptomvces scabies, and sweet potato pox
by S. ipomoeae. Some are cause oI inIections oI humans and animals e.g. Nocardia asteroides and
N.otitidis caviarum. Most oI the actinomycetes inhabitate in soil under aerobic conditions. These
actinomycetes can be divided into only a Iew Iamilies as given in Figure 2.12.


Actinomycetes 7 Iamilies
1. Streptomycetaceae
Streptomyces (Chitin hydrolizing, Liberate enzymes which lyse the bacteria)
Microellobosporia
Sporichthya
2. Nocardiaceae
Nocardia
Pseudonocardia
3. Micromonosporaceae
Micromonospora (decompose chitin, cellulose, glucosides and hemicelluloscs)
Microbispora
Micropolyspora
Thermomonospora
Thermoactinomyces
ActinobiIida
4. Actinoplanaceae
Streptosporangium
Actinoplanes
Planobispora
Dactylosporangium
5. Dermatophilaceae
Geodermatophilus
6. Frankiaceae
Frankia
7. Actinomycetaeae
Actinoinyces

Figure 2.12: Schematic description of the major groups of Actinomycetes.


Bacteria are unicellular prokaryotic microorganisms, one oI the simplest and smallest Iorms oI liIe
known. Their capacity Ior rapid growth allows bacteria to adjust their activities quickly in pesponse
to changes in their environment. Bacterial size seldom exceeds 4-5 m (0.004-0.005 mm) in length.
The shape oI bacteria varies in that they may be nearly round (coccus), rod-like (bacillus), spiral
(spirillum), or curved (vibrio). The bacilli seem to be predominate in the soil. Bacteria are either
autotrophic (obtain their energy Irom the oxidation oI inorganic substances such as ammonium,
sulIur or iron, and most oI their carbon Irom CO
2
), or heterotrophic (get their energy and carbon
Irom the breakdown oI organic matter). Bacteria participate vigorously in all oI the organic
transactions. They also dominate in several basic enzymatic transIormations e.g. nitriIication, sulIur
oxidation and nitrogen-Iixation etc. The bacteria have a number oI beneIicial.eIIects in our daily
liIe like Iermentation processes in Iood industry, decompostion oI organic wastes, plant nutrients
recycling, pest control, environmental pollution control, in the Ieed oI ruminents etc.
General schemes Ior the classiIication oI bacteria are based upon nutritional patterns, oxygen needs,
and symbiotic relationships. They are Iurther deIined as phot-or chemo-to designate their energy
source. The schematic classiIication oI bacteria alongwith some characteristics is given in Figure
2.13. Bacteria are placed in a single class Schizomycetes and classiIied into 10 orders according to
the Bergey' s Manual.

Monera
1. Schizophyceae (blue-green algae) l
2. Schizomycetes (bacteria) - 10 orders
2.1 Pseudomonadales
2 sub-orders. Gram -ve, rarely occur in pairs or chains, cells usually polar Ilagellate, Phot
autotrophic as well as heterotrophic species. No endospores are Iound; reproduction by Iission.
Some are parasitic, some pathogenic.
2.2 Chlamydobacteriales
3 Iamilies, Gram -ve; colourless, alga-lake bacteria which occur in trichomes. May or may not
be ensheathed composed oI organic matrix with Fe or Mn oxides or Iree oI these oxides.
Endospore never developed. Freshwater or marine Iorms.
2.3 Hyphomicrobiales
Gram -ve; heterotrophic or phototrophic; Iound in mud, water oI Ireshwater ponds and streams,
parasitic on Ireshwater crustacea.
2.4 Eubacteriales
Gram -ve/ve; pigments nonphotosynthetic; saprophytic/parasitic and many pathogenic; Iound
every where.
2.5 Actinomycetales
Elongated cells (hyphae); cell structure like bacteria; cell-wall not oI chitin or cellulose; a Iew
pathogenic; Iound in soil and Ireshwater.
2.6 Caryophanales
Occur as trichomes (many-celled Iilaments) or as shorter structures; Iound in water, the
intestine oI arthropods and vertebrates, and in decomposing OM.
2.7 Beggiatoales
Trichomes in 3 Iamilies and not in 4th Iamily; no Ilagella, no chlorophyl; Iound in Ireshwater,
marine habitats, in soil and in decomposing OM, especially algae.
2.8 Myxobacterales
Flexible rods, which multiply by binary, transverse Iission; actively motile cells as groups oI
two to several hundred individuals; moving cells may have the substrate.
2.9 Spirochaetales
Slender; Ilexuous motile; multiplication by transverse Iission; Iree-living, saprophytic, and
parasitic Iorms.
2.10 Mycoplasmatales
Nonmotile; typical endospores never produced; grows in agar media; pathogenic and
saprophyiic species occur.
3. Microtatabiotes (Viruses and others)

Figure 2.13: Schematic description of the major groups of the division Protophyta (Kingdom
Monera).

Sub-order 1.1. Rhodobacteriineae
(Contain red, purple, brown or green photosynthetic pignents. Sometimes also enclose granules oI
Iree sulIur)
1.1.1 Thiorhodaceae
Anaerobic or microaerophilic with a photosynthetic metabolism in which CO
2
is reduced. H
2
S acts
as H

donor, and S accumulates as S droplets in the cells. Can also utilize OM in place oI H
2
S Ior
photosyihesis. Potentially mixotrophic.
Thiosarcina
Thiopedia
Thiocapsa
Thiodictyan
Thiothece
Thiocystis
Lamprocystis
Amoebobacter
Thiopolycoccus
Thiospirillum
Rhabdomonas
Rhodothece
Chromatium
1.1.2 Anthiorhodaceae
Generally microaerophilic, although many members may grow at Iull atmospheric. O
2
tension.
Capable oI development under strictly anaerobic conditions, but only in illuminated cultures by
virtue oI the photosynthetic metabolism. Latter dependent upon the presence oI alcohols, Iatty acids,
hydroxy- and keto-acids. Members which can grow in presence oI air can also be cultivated in
darkness, but only under aerobic conditions.
Rhodopseudomonas
Rhodospirillum
1.1.3 Chlorobacteriaceae
Contain green pigments oI a chlorophyllous nature, capable oI photosynthesis in the presence oI
H
2
S; do not liberate O
2
.
Chlorobium
Pelodictyon
Chlathrochloris
Chlorobacterium
Chlorochromatium
Cylindrogloea

Figure 2.14: Schematic description of the major groups of sub-order Rhodobacteriineae.

Sub-order 1.2. Pseudomonadineae
(Gram -ve; do not have photosynthetic pigments but diIIusible, water-soluble pignents. Some are
autotrophic, others are heterotrophic. A Iew spp. are strictly anaerobic. Parasitic, a Iew pathogenic
to vertebrates. 7 Iamilies
1.2.1 Nitrobacteriaceae
Gram -ve; derive energy Irom oxidation oI ammonia to nitrite or Irom nitrite to nitrate; depend
upon this oxidation Ior growth. Not parasitic; Iound in soil and Ireshwater.
Nitrosomonas.
Nitrosococcus
Nitrosospira
Nitrosocystis
Nitrosogloea
Nitrobacter
Nitrocystis
1.2.2 Methanomonadaceae
Gram -ve; rod-shaped, derive energy Irom the oxidation oI compounds oI H or C. Found in soil and
water.
Methanomonas (Oxidize methane)
Hydrogenomonas (Oxidize hydrogen)
Carboxydomonas (Oxidize carbon monoxide)
1.2.3 Thiobacteriaceae
Presumably gram -ve; oxidize sulIur, colourless, neveI Iilamentous. Found where H
2
S occurs, or
may oxidize Iree S, thiosulIates or related compounds.
Thiobacterium
Macromonas
Thiovulum
Thiospira
Theobaciilus (oxidize Iree S, and thiosulIates; autotrophic or Iacultative autotrophic)
1.2.4 Pseudomonadaceae
Gram ve; aerobic; Irequently oxidative, but may be Iermentative, usually Iound in soil or water.
Many plant and a Iew animal pathogens.
Pseudomonas
Xanthomonas
Acetobacter (vinegar bacteria)
Aeromonas
Photobacterium
Azotomonas
Zymomonas
Protaminobacter
Alginomonas
Mycoplana
Zoogloea
Halobacterium
1.2.5 Caulobacteraceae
Gram -ve; Non-Iilamentous; cells are polar Ilagellate; multiply by transverse Iission. Typically
Ireshwater or saltwater Iorms.
Caulobacter
Gallionella
Siderophacus
Nevskia
1.2.6 Siderocapsacete
Polar Ilagellate; Iree-living in surIace Iilms or attached to the surIace oI submerged objects.
Autotrophic, Iacultatively auto-trophic and heterotrophic Iamily. Found in Ireshwater. Form
deposits oI Fe and Mn compounds.
Siderocapsa
Siderosphaera
Sideronema
Ferribacterium
Sideromonas
Naumanneilla
Ochrobium
Siderococcus
Siderobacter (Iound in neutral or alkaline waters)
Ferrobacillus (Iound in acid mine wastes).
1.2.7 Spirillaceae
Gram -ve; single Ilagellum (rarely two). Frequently oxidative; aerobic or Iacultative anaerobic, a
Iew strict anaerobes; largely Iorms, some are parastic or pathogenic to higher animals or man.
Vibrio
DesulIovibrio (reduce sulIates to H
2
S)
Methanobactcrium (reduce CO
2
to methane)
Cellvibrio (attack cellulose)
CellIalcicula
Microcyclus
Spirillum
Paraspirillum
Selenomonas
Myconostoc

Figure 2.15: Schematic description of the major groups of sub-order Pseudomonadineae.

Order 2. Chlamydobacteriales 3 Iamilies
2.1 Chlamydobacteriaceae
Occur in trichomes which show Ialse branching. Cells divide transversely. Usually Iound in
Ireshwater.
Sphaerotilus
Leptothrix
Toxothrix
2.2 Peloplocaceae
Long, unbranched trichomes; generally non-motile; reproduction by transverse Iission. Unattached
Iorms Iound in Ireshwater ponds with decomposing algae.
Peloploca
Pelonema
2.3 Crenotrichaceae
Trichomes attached to a Iirm substrate. Cells disk-shaped to cylinderical, dividing to produce
spherical, nonmotile conidia. Found in Ireshwater and saltwater.
Crenothrix
Phragnidiothrix
Clonothrix

Figure 2.16: Schematic description of the major gronps of the order Chlamydobacteriales.


Order 3. Hyphomicrobiales 2 Iamilies
3.1 Hyphomicrobiaceae
Gram -ve; occur mainly as Iree-Iloating groups. Daughter-cell Iormation initiated by the outgrowth
oI a Iilament Irom the pole oI a mature cell. Daughter cell is Iormed by enlargement oI the tip oI
the Iilament.
Hyphomicrobium (motile, chemoheterotrophic)
Rhodomicrobium (non-motile, photoheterotrphic)
3.2 Pasteuriaceae
Stalked with spherical or pear-shaped cells, stalks may be very short or absent. Cells multiply by
longitudinal Iission and/or by budding. Mostly periphytic; one species parasitic.
Pasteuria
Blastocaulis

Figure 2.17: Schematic description of the major groups of the order Hyphomicrobiales.

Order 4. Eubacteriales 13 Iamilies
4.1 Azotobacteraceae
Gram -ve; relatively large lods or even cocci, cells without endspores. Flagellation is peritrichous.
Obligate aerobes; Iix atm. N. Found in soil and water.
Azotobacter
4.2 Rhizobiaceae
Usually gram -ve; cells without endospores, rod-shaped, sparsely Ilagellated; some spp. non motile.
Grow aerobically; saprophytes, symbionts and pathogens.
Rhizobium (Iix N on the roots oI leguminosae)
Agrobacterium (donot Iix N; either plant pathogen on roots/stem or Iree living
non-chromogenic in soil or water)
Chromobacterium (Iree living in soil and water, produce a violet chromogenesis)
4.3 Achromobacteriaceae
Gram -ve; small to medium-sized rods; motile by paritrichous Ilagella, or non-motile. May produce
acid but no gas Irom glucose/sugars; lactose rarely attacked; Iound in saltwater, Ireshwater or soil,
less commonly as parasites or pathogens.
Alcaligenes
Achromobacter
Flavobacterium
Agarbacterium (attack agar and/or alginates)
Beneckea (attack chitin and sometimes horny substances)
4.4 Enterobacteriaceae
Consists oI 5 Tribes. Gram -ve; straight rods. All species attack glucose producing acid or acid and
gas; nitrites produced Irom nitrates. Some spp. attack alginates or pectins. Many spp. live in the
intestines oI man and other animals causing disturbances; others parasitic on plants; some
saprophylic.
Tribes genera
Escherichieae
Escherichia
Aerobacter
Klebsiella
Alginobacter
Erwinieae
Erwinia
Serratieae
Serratia
Proteeae
Proteus
Salmonelleae
Salmonella
Shigella
4.5 Brucellaceae
Gram -ve; Aerobic, Iacultatively anaerobic; some invade living tissues; parasites and pathogens to
warm-blooded animals.
Pasteurella (attack CH
2
O)
Bordetella (donot attack CH
2
O)
Brucella
Haemophilus
Actinobacillus
Calymmatobacterium
Moraxella
Boraxella
Bordetella
Noguchia
4.6 Bacteroidaceae
Gram -ve; rods; Ierment simple CH
2
O to acid, gas may be produced; normally strict anaerobes,
occasionally microaerophilic; Iound in intestinal tract oI warm-blooded animals; sometimes
pathogenic.
Bacteroides
Fusobacterium
Dialister
Sphaerophorus (strict anaerobes)
Streptobacillus (Iacultative anaerobes)
4.7 Micrococcaceae
Gram ve/-ve; endospores not produced except in Sarcina ureae; Motility rare; heterotrophic.
Free-living saprophytic to parasitic or even pathogenic; Anaerobes live in decomposing organic
matter.
Micrococcus (oxidative aerobic)
Staphylococcus (Iacultatively anaerobic)
GaIIkya (Non-motile)
Sarcina (usually nonmotile)
Methanococcus (produce CH
4
Irom OM)
Peptococcus (donot produce CH
4
)
4.8 Neisseriaceae
Gram -ve; spherical; in pairs, nonmotile; aerobic, Iacultatively anaerobic and anaerobic. Optimum
temp. 37C. All spp. parasitic.
Nesseria (Aerobic or Iacultatively anaerobic)
Veillonella (Anaerobic)
4.9 Brevibacteriaceae
Gram ve; cells without endospores; Aerobic and Iacultatively anaerobic; Iound in dairy products,
soil, saltwater, Ireshwater and decomposing substances.
Brevibacterium (acid produced Irom simple CH
2
O)
Kurthia (CH
2
O are not utilized)
4.10 Lactobacillaceae
Has 2 tribes, gram ve, CH
2
O essential Ior growth which are Iermented to lactic acid, alcohol and
CO
2
. Microaerophilic to anaerobic; Iound in mouth and intestinal tract oI man and animals, in Iood,
dairy products; Iermenting vegetable juices. A Iew highly pathogenic.
Tribes genera
Streptococceae
Diplococcus
Streptococcus
Pediococcus
Leuconostoc
Peptostreptococcus
Lactobacilleae
Lactobacillus
Eubacterium
Catenabacterium
Ramibacterium
Cillobacterium
4.11 Propionibacteriaceae
Gram ve; nonmotile. non-proteolytic, usually saccharolytic, Ierment CH
2
O to lactic acid;
anaerobic to aerotolerant. Inhabitants oI intestinal tracts oI animals, also occur where suitable Iood
stuIIs are Iound
Propionibacterium (produce propionic and acetic acids and CO
2
)
Butyribacterium (produce butyric and acetic acids and CO
2
)
Zymobacterium (CH
2
O Iermented, glucose converted to ethanol and CO
2
)
4.12 Corynebacteriaceae
Generaly gram ve; usually nonmotile rods; aerobic to microaerophilic. a Iew anaerobic; animal
and plant parasites/pathogens, also Iound in dairy products and soil.
Corynebacterium
Listeria
Erysipelothrix
Microbacterium (saprophytic)
Cellulomonas (decompose cellulose)
Arthrobacter
4.13 Bacillaceae
Usually gram ve; rod-shaped, produce endospores, Ierment sugars; aerobic, Iaculta-tively
anaerobic, anaerobic or aerotolerant, may grow at 55C; mostly saprophytic in soil, a Iew
parasites/pathogens oI animals or insects.
Bacillus (aerobic or Iacultatively anaerobic)
Clostridium (anaerobic or aerotolerant)

Figure 2.18: Schematic description of the major groups of the order Eubacteriales.

Order 5. Actinomycetales 4 Iamilies
5.1 Mycobacteriaceae
Gram ve; cells spherical to rod-shaped; no conidia; aerobic; mesophilic; Iound in soil, dairy
products, and parasites on animals and man.
Mycobacterium (acid-Iast)
Mycococcus (non acid-Iast)
5.2 Actinomycetaceae
Some spp. partially acid-Iast; Iorm a true mycellium; obligately aerobic, anaerobic or
microaerophilic.
Nocardia
Actinomyces
5.3 Streptomycetaceae
Conidia borne on sporangiophores; Iound in soil, sometimes thermophilic in rotting manure, a Iew
spp. are parasitic.
Streptomyces
Micromonospora
Thermoactinomyces (growth occurs between 50 and 65C)
5.4 Actinoplanaceae
Reproduction by spores Iormed in sporangia; conidia Iormed in many spp.; widely distributed in
soil and Ireshwater.
Actinoplanes
Streptosporangium

Figure 2.19: Schematic description of the major groups of the order Actinomycetales.


Order 6. Caryophanales 3 Iamilies
6.1 Caryophanaceae
Large trichomes and Iorm no spores; Iound on the mucous membranes oI the oral cavity oI man
and various other animals, in the alimentary tract oI ruminants and in decomposing organic
materials.
Caryophanon
Lineola
Simonsiella (Iound in the buccal cavities oI vertebrates)
6.2 Oscillospiraceae
Occur in trichomes; spores are Iormed by a Iusion oI the protoplasms oI 2-3 neighboring cells;
actively motile by peritrichous Ilagella or nonmotile; parasitic in the intestinal tracts oI vertebrates.
Oscillospira
6.3 Arthromitaceae
Trichomes probably divided into cells although septa disappear during sporulation. Spores Iorm in
the distal ends oI trichomes. Nonmotile. Trichomes are attached by a spherical body in groups to
the intestinal walls oI insects, crustaceans, and tadpoles.
Arthromitus
Colemitus

Figure 2.20: Schematic description of the major groups of the order Caryophanales.


Order 7. Beggiatoales 4 Iamilies
7.1 Beggiatoaceae
Individual cells, occur in trichomes, no chlorophyll and phycocyanin; when grow in the presence oI
H
2
S, the trichomes contain sulIur globules.
Beggiatoa
Thiospirillopsis
Thioploca
Thiothrix
7.2 Vitreoscillaceae
Gram -ve; colourless trichomes showing gliding motion; no chlorophyll or phycocyanin; donot
hydrolyze proteins; Iound in dung, soil, water with decaying plant material, in myxophycean scum
on the surIaces oI quiet water.
Vitreoscilla
Bactoscilla
Microscilla
7.3 Leucotrichaceae
Short, cylinderical cells arranged in nonmotile trichomes; strictly aerobic; resemble BGA in many
respects but lack photosynthetic pigments; Iound in Ireshwater, saltwater having decomposing
algae material.
Leucothrix
7.4 Achromatiaceae
Large, unicellular organisms which are spherical to ovoid or shortly cylindrical; no special organs
oI locomotion; Do not possess photosynthetic pigments. Found in Iresh-water and marine
environ-ments.
Achromatium

Figure 2.21: Schematic description of the major groups of the order Beggiatoales.

Order 8. Myxobacterales 5 Iamilies
8.1 Cytophagaceae
Flexible, sometimes pointed rods showing gliding motility. No Iruiting bodies or resting cells
(microcysts) are Iormed.
Cyiophaga
8.2 Archangiaceae
Resting cells are shortened rods, never enclosed in larger cysts. Fruiting bodies are irregularly
swollen or twisted, or are Iinger-like structures.
Archangium
Stelagium
8.3 Sorangiaceae
Shortened rods oI the Iruiting body. Cysts are surrounded by a membrance. Primary cyst may be
diIIerentated Irom the angular or secondary cysts. No stalked Iorms are known.
Sorangium
8.4 Polyangiaceae
Resting cells enclosed in cysts which can occur either singly or in clusters at the tips oI the stalks.
Cysts may be sessile, occuring either singly or in groups and developed in a slime membrane, or
they may be raised on stalks (cystophores).
Polyangium
Synangium
Podangium
ChondIomyces
8.5 Myxococcaceae
The rods become shortened when Iruiting occurs and develop into spherical or ellipsoidal
microcysts. DeIinite Iruiting bodies are produced except in sporocytophaga genus.
Myxococcus
Chondrococcus
Angiococcus
Sporocyiophaga

Figure 2.22: Schematic description of the major groups of the order Myxobacterales.

Order 9. Spirochaetales 2 Iamilies
9.1 Spirochaetaceae
Coarse, spiral organisms possessing deIinite protoplasmic structures. Found in stagnant Ireshwater
or saltwater, and in the intestinal tract oI bivalve molluses.
Spirochaeta
Saprospira
Cristispira
9.2 Treponemataceae
Coarse or slender spirals; protoplasm possesses no obvious structural Ieatures. Many oI these can
be cultivated. With Iew exceptions, parasitic in vertebrates. Some are pathogenic.
Borrelia
Treponema (anaerobic)
Leptospira (aerobic)


Order 10. Mycoplasmatales only one Iamily
10.1 Mycoplasmataceae
Characteristics same as Ior the order.
Mycoplasma

Figure 2.23: Schematic description of the major groups of the order Spirochaetales and
Mycoplasmatales.
MICROTATOBIOTES
It is the third class oI the Division Protophyta, and it includes the smallest oI the living things e.g.
Rickettsia, and viruses. All are maniIested by a dependence on the living organisms Ior their
growth and multiplication. Parasitism is axiomatic since there is no way to determine iI there are
Iree-living Iorms. Most oI these organisms occur intracellularly; Ricketlsia quintana Schmincke oI
trench Iever is an example oI extracellular growth in its host, the body louse. A Iew oI the visible
Iorms are known to occur intranuclearly. Some species utilize both intermediate and deIinitive
hosts Ior their propagation. The largest members are the rickettsia-like organisms which are oIten
pleomorphic, including coccoid to Iilamentous Iorms, while others show morula-like clusters oI
elementary bodies occuring at one or upto twenty colonies in an inIected cell. The small members
grade downward to Iilterable virus particles susceptible oI measurement only by physio-chemical.
techniques and by special preparation under the electron microscobe. The detailed classiIication oI
these microorganisms is given in the Figure 2.24.

VIRUS
Luria and Darnell (1968) deIined the virus as, "viruses are entities whose genome is a nucleic acid,
either DNA or RNA which reproduce inside living cells and use their synthetic machinery to direct
the synthesis oI specialized particles- the Virions, which contain the viral genome and transIer it to,
other cells". The virion is a technical term Ior the virus. A virion consists oI nucleic acid
surrounded by a protein coat. The nucleic acid is called Nucleoid (which may be DNA or RNA,
never both) and Iorms the genome. In animal and bacterial viruses (bacterio-phages), the nucleic
acid is DNA while in plant viruses it is always RNA. The protein coat is called Capsid. Viruses
diIIer Irom Rickettsiae and the Pittacosis group oI organisms, (which are also obligate intracellular
parasites) in the Iollowing respects.
1. Viruses contain either DNA or RNA, never both.
2. Virus protein are synthe,sized on the host ribosomes.
3. Viruses multiply by independent synthesis oI their constituents, nucleic acid and proteins,
and their assembly rather than by growth and division.
Earlier, the viruses were classiIied on the basis oI their hosts, as plant viruses, animal viruses, and
bacterial viruses (bacteriophages). AIterwards, a new classiIication was proposed by Andre LwoII
and Tournier in 1966, which has been accepted by the Provisional Committee on Nomenclature oI
Viruses (PCNV); it is given in Figure 2.25.
Viruses have limited organisms that can act as hosts as they parasitize only speciIic plants, animals,
or other organisms. Sometimes a second virus is essential beIore the Iirst can replicate. There is
almost no chemical control Ior the virus inIection. They can be controlled to some extent by
removing the host carriers like nematodes, Iungi, and roots oI some plants. A Iew viruses
over-winter in soil but are commonly hosted and disseminated by nematodes or Iungi. Common
plant viruses in soil may survive only about 1 to 4 weeks. Enzymes in the soil attack viruses, so
they are not viable in soils Ior long periods oI time.

Class Microtatoblotes
1. Rickettsia
Gram -ve; small; rod-shaped coccoids; oIten pleomorphic organisms occuring as elementary bodies,
usually intracellular but occasionally be Iacultatively or exclusively extracellular. Usually
nonIilterable; parasitic, may cause diseases in man and other animals; seldom kill the invertebrate
hosts. 4 classes
1.1 Rickettsiaceae
Gram -ve ; oIten associated with arthropod tissues; pathogenic, parasitic.
Tribes genera
Rickettsieae
Rickettsia
Coxiellu
Ehrlichieae
Ehrlichica
Cowdria
Neorickettsia
Wolbachieae
Wolbaehia
Symbictes
Rickettsiella
1.2 Chlamydiaceae
Gram -ve; obligate, intracytoplasmic parasites or saprophyies; pathogenic in various
warm-blooded animals.
Chlamydia
Colesiota
Ricolesia
Colettsia
Miyagawanella
1.3 Bartonellaceae
Gram -ve; parsites oI the erythlocytes in man and other vertebrates; not acid-Iast, parasitic and
pathogenic to vertebrates.
Bartonella
Grahamella
Haemobartonella
Eperythrozoom
1.4 Anaplasmataceae
Parasitize red blood cells; parasites oI ruminants, transmitted by arthropods, multiply in red
blood cells; produce disease in non-splenectomized and in splenectomizod ruminants.
Anaplasma
2. Virales
Viruses are etiological agents oI disease, typically oI small size and capable oI passing Iilters that
retain bacteria, increasing only in the presence oI living cells, giving rise to new strains by mutation.
Viruses cause diseases oI bacteria, plants and animals. They are diIIicult to cultivate. They are
composed oI nucleic acids and proteins.
Animal viruses (pathogen to man and animals)
plant viruses (pathogen to palnts)
Bacterio-phages (attack bacterial cell)

Figure 2.24: Schematic description of the major groups of class Microtatobiotes.



Phylum VIRA
1. Deoxyvira (containing DNA)
Deoxyhelica
Chaetovirales
Deoxycubica
Haplovirales
Deoxybinala
Urovirales
2. Ribovira (containing RNA)
Ribohelica 2 orders
Rhabdovirales
Sagovirales
Ribocubica 2 orders
Gymnovirales
Tagovirales

Figure 2.25: Schematic description of the major groups of the phylum Vira (viruses).
Chapter 3
MICROBIAL NUTRITION

The major Iactor determining whether or not a microbe will grow in a particular environment, is the
availability oI suitable nutrients. The microorganisms are nutritionally much more diverse than
macroorganisms. There has been much interest recently in the microbial degradation oI a wide
range oI natural and artiIicial chemicals, both with a view to recycle the wastes and with a view to
prevent biodeterioration. Many microorganisms, particularly the bacteria, have or can acquire the
ability to utilize novel or unusual chemicals. There are Iour useIul ways to classiIy potential
nutrient molecules as;
1. essential, or useIul but dispensable,
2. building blocks Ior macromolecules, or as energy source, or as both,
3. macronutrients required in large quantities, or as micronutrients, and
4. macromolecules requiring breakdown beIore entry to the cell or as small molecules readily
entering as soluble nutrients.
In the microbial cell, the major elements are carbon, hydrogen, oxygen, nitrogen, sulIur and
phosphorus, together with minerals. The ubiquitous source oI carbon is CO
2
. This is utilized as sole
carbon source only by autotrophs but all organisms probably incorporate some via anaplerotic
pathways. Monosaccharides, such as glucose, are rarely Iound in nature, probably because they are
so rapidly taken up by microbes. They are incorporated directly into macromolecules and can act as
good energy sources. Disaccharides such as lactose and sucrose are more commonly Iound, and
their utilization depends on the ability oI the cell to produce an enzyme to hydrolyse the glycosidic
bond. Most oI the carbohydrate in nature is in the Iorm oI polysaccharides. Cellulose and chitin are
very abundant in soil, but are intractable molecules, being only slowly attacked by hydrolytic
enzymes to yield soluble sugars. The ability to utilize a particular polysaccharide is oIten a Iairly
restricted phenomenon. Thus celluloses are common in Iungi, but more unusual in bacteria, Ior
example being produced by myxobacteria, and some species oI Bacillus, Cellvibrio, Cvtophaga,
Pseudomonas, Clostridium and the actinomycetes. The anaerobic digestion oI cellulose is very
important in the rumen and in deep sediments. Organic acids are readily used directly as carbon
sources by most microbes. Fats are digested by lipases to give glycerol and Iatty acids, and
organisms with this ability are important as Iood spoilage organisms. Hydrocarbons, Irom methane
through to petroleum, Iorm a discrete group oI carbon sources. Organisms utilizing them are oI
importance to man by degrading Iuels and subsequently blocking Iuel lines, but also by utilizing
petroleum wastes to give 'single-cell protein'. Proteins and their constituent amino acids are utilized
as carbon sources by proteolytic organisms, such as Pseudomonas spp. Iound as Iood spoilage
organisms and Staphvlococcus spp. Iound as human pathogens.
Only a Iew prokaryotic organisms, such as A:otobacter and Rhi:obium spp. and some blue-green
algae, can utilize the gaseous dinitrogen (N
2
). Nitrate is Iound in acrobic soils and waters, but not
all aerobic organisms have the necessary nitrate reductase with which to utilize it. Ammonia is
more readily utilized; in higher concentrations via the ubiquitous glutamate dehydrogenase, in
lower concentrations via the less common glutamate synthase. Amino acids, nucleotides, uric acid
and urea can also provide microbial cell's requirement Ior nitrogen. SulIur occurs widely in nature
as sulIate, which is reduced via sulIide to be incorporated into the sulIur-containing amino acids
and coIactors. Some organisms can utilize H
2
S as source oI sulIur. Organic sulIur, as amino acids
cysteine and methionine, can also be used. Phosphates are very common in nature, but are oIten
largely unavailable as they are in the Iorm oI insoluble metal phosphates. Probably all organisms
can utilize soluble inorganic phosphates, and many produce phosphatases that will hydrolyse
organic phosphates in the environment. OI the minerals, relatively large amounts oI potassium,
magnesium and iron are required by virtually all microbes, while some require calcium (e,g.
Bacillus spp. Ior spore Iormation), sodium (e.g. the halophytes), or silicon (e.g. diatoms). The
requirements and Iunctions oI trace metals have proved diIIicult to determine, as they are
commonly present as contaminants. It is doubtIul iI the presence or absence oI the cations
commonly required Ior growth, zinc, copper, cobalt, manganese, molybdenum, is oIten an
important ecological determinants. It has oIten been suggested that the availability oI vitamins can
be an important ecological Iactor. Over halI oI the planktonic algae tested require vitamin B
12

(vitamins A, C and D are not required by Iungi and bacteria), while other algal species and bacteria
wtll release it. Thus the cycling oI this vitamin could be controlling Iactors in the succession oI
species in plankton blooms.


CLASSIFICATION OF MICROBES ON THE BASIS OF NUTRITION
Microorganisms can be classiIied into various groupings according to their nutrition. This
classiIication depends on the organism's source oI energy, carbon and reducing equivalents. Such a
classiIication is particularly useIul in the present context as it bypasses the concept oI species and
genus, and concentrates rather on the chemical activities oI the organisms. Like most taxonomic
schemes, however, there are limits to its useIulness. These limits are most oIten overstepped when
too rigid a deIinition oI a term is proposed.
The micluorganisms are divided into three major groups on the basis oI their nutridonal pattern,
these main groups are still sub-divided due to some additional phenomena oI the microbes. The
main groups are:
A: Strict Autotrophs
These organisms cannot utilize organic matter and may even be harmed by its presence. They are
able to synthesize complex compounds composing their protoplasm Irom simple inorganic salts.
They obtain their carbon Irom CO
2
and their energy Irom the oxidation oI certain inorganic
compounds or even elements. Because oI this Iact, they are independent oI vegetable and animal
liIe. Green plants are the typical autotrophs.
B: Strict Heterotrophs
They cannot synthesize their complex protoplasm Irom simple inorganic salts but must have
organic compounds, such as proteins, peptones, amino acids, and vitamins, Ior growth. Animals are
the typical heterotrophs.
C: Facultative Organisms
The Iacultative heterotrophs show characteristics intermediate between the two, being able to
utilize both inorganic and organic compounds. They comprise the great majority oI bacteria.
BeIore discussing the microbial nutrition, Iirst we have to deIine a Iew other modes oI nutrition in
microorganisms. Originally biologists recognized these two main types oI nutrition viz. autotrophic,
and heterotrophic. However, now it is known that a sharp distinction can not be made between the
two types. Even the typical autotrophs like the green plants require speciIic growth Iactors which
are organic compounds. Thus, new nutritional classiIications have been made. II the need Ior the
growth Iactor is disregarded, the organisms can be classiIied on the basis oI the energy source viz.
light or chemical oxidation which are the ultimate sources oI energy Ior all organisms. There are
two groups on the basis oI their energy source as under:
Phototrophs:
The organisms which possess chlorophyll and use sun light are called phototrophs or
photosynthetic.
Chemotrophs:
The organisms which use chemical energy by oxidizing inorganic compound like ammonia, nitrate,
nitrite, sulIur or Ierrous iron, are known as chemotrophs or chemosynthetic.
Another classiIication can be made on the basis oI the source oI the electron or reducing
equivalents, inorganic or organic compounds. There are two types on this basis as:
Lithotrophs:
They produce the reducing equivalents (electrons) required Ior cell synthesis Irom inorganic
materials such as H
2
S, Ierrous iron, ammonia and sulIur.
Organotrophs:
These organisms can only derive their electrons (reducing power) Irom the oxidation oI organic
nutrients.
Based on the above mechanisms oI nutrition, the modes oI nutrition in Iungi and bacteria have been
described in the Iollowings.


FUNGAL NUTRITION
Fungi are heterotrophic organisms deriving their nutrition Irom external sources. The Iungi have
Absorptive or Holophytic type oI nutrition. The substrate is dissolved and then absorbed. For this,
the Iungi produce extracellular enzymes which degrade the insoluble substrate into smaller
Iragments and Iinally into soluble units which are then absorbed by the hyphae. The Iungi live as
parasites (Ieed upon other living organisms), saprophytes (Ieed on dead organic matter), or
symbionts (have mutual cooperation with other organisms). As parasites, Iungi grow on plants,
animals and human beings causing diseases by their presence. Fungal parasitism varies Irom
Iacultative parasitism to obligate parasitism. The Iacultative parasites can grow saprophytically in
the absence oI the host while obligate parasites (downy mildews, powdery mildews and rusts) grow
only on their speciIic hosts. All the classes oI Iungi include important plant pathogens. Fungi, in
general, are not important parasites oI human beings.
When Iungi grow on dead organic matter ther are called saprophytes. Here also, the saprophytism
may vary Irom Iacultative saprophytism to obligate saprophytism. They have poor or no parasitic
ability, respectively. Some Iungi lie in the soil on a piece oI dead leaI but they cannot grow even
little in the soil. Strong saprophytes produce antibiotics and Iungistatic substances in the soil, which
do not allow the growth oI other Iungi especially the parasites. This is called antibiosis or
mycostasis. There is competition everywhere, and it occurs in soil also. A teaspoonIul oI soil
contains millions oI organisms and thus they have an acute house problem. There is struggle Ior
existence; one prevents the growth oI the other. Like ours, theirs is also a busy, vexed, quarrelsome
world. But there, survival is oI the Iittest only.
Saprophytic Iungi are indispensible in the maintenance oI the carbon and mineral cycles in nature,
and the decomposition oI cellulose and lignin present in the dead vegetation. Fungi enter into
permanent association with other organisms in which both partners beneIit. This is called symbiosis.
The Lichins and Mycorrhiza are such symbiotic relations oI Iungi. In lichins, they are the partners
with algae. In mycorrhiza (meaning 'Iungus root') the Iungal hyphae Iorm a compact
pseudoparenchymatous mantle ardund the roots oI some vascular plants like Pinus, and also extend
into the cortex. The mycorrhiza help in absorption oI minerals. The Iungus mantle acts as a water
sponge. Some plants would not grow until their roots have come in touch with the mycorrizal Iungi.


BACTERIAL NUTRITION
There is a great diversity in bacteria according to their nutritional requirements. For their nutritional
classiIication, a synthesis oI the three criteria viz. carbon source, energy source and electron donor,
can be used. In this way the Iollowing Iour nutritional groups emerge.
1. Photosynthetic Autotrophic Bacteria
These can also be said as Photolithotrophs. These are the photosynthetic bacteria which use
inorganic electron donor H
2
, H
2
S, NH
3
, S etc. (but never H
2
O) Ior reduction oI CO
2
to organic
compounds. For example, green sulIur bacteria (Chlorobacteriaceae), purple sulIur bacteria
(Thiorhodaceae). Because oI the non-utilization oI water as electron source, O
2
is never evolved
during bacterial photosynthesis.
2. Photosynthetic Heterotrophic Bacteria
Also known as Photoorganotrophs or photosynthetic bacteria, these are the bacteria with the
diIIerence that instead oI inorganic substances, organic substrates supply the electrons Ior reducing
CO
2
in the presence oI sunlight, e.g. non-sulIur bacteria. Thus here also the O
2
is not evolved.
3. Chemosynthetic Autotrophic Bacteria
These bacteria are also called as Cbemolithotropbs. No organisms other than some bacteria come in
this nutritional category. They derive their energy Ior growth Irom oxidation oI inorganic
substances. A number oI specialized groups oI bacteria belong to this category e.g., the hydrogen
bacteria, the colourless sulIur bacteria, nitriIying bacteria, iron bacteria etc. Most oI them are
autotrophic and use CO
2
as the source oI carbon. All the energy-yielding reactions oI
chemolithotrophic bacteria are oxidation-reduction reactions in which the hydrogen or electrons are
transIerred Irom one compound to another. The accepter oI the electron may be oxygen or another
inorganic substance. The energy is trapped in ATP molecules during the transport oI hydrogen to
the oxygen, as it occurs during respiration oI organic compounds. This type oI bacteria are Iurther
classiIied as:
3.1 Hydrogen bacteria:
These oxidize hydrogen in the presence oI oxygen e.g. Hydrogenomonas.
H
2

1/2
O
2
--- H
2
O Energy
The key reaction in the oxidation oI hydrogen is splitting oI molecules into two hydrogen atoms by
the enzyme hydrogenase.
3.2 Nitrifying bacteria:
The oxidation oI ammonia into nitrate occurs in two steps, each carried out by a specialized group
oI bacteria.
a) In the Iirst step ammonia is oxidized into nitrite by species oI the genus Nitrosomonas. The
energy librated is the sole source oI energy Ior the growth oI the bacteria. The carbon is obtained
Irom CO
2
.
NH
3
1
1/2
O
2
--- NO
2
-
H
2
O H

Energy
b) In the second step, the nitrite is converted into nitrate. This is brought about by species oI the
genus Nitrobacter, which use this energy Ior growth. Here also carbon is derived Irom CO
2
.
NO
2

l/2
O
2
--- NO
3
-
Energy
3.3 Sulfur bacteria:
a) Oxidation oI elemental sulIur
Thiobacillus thio-oxidans obtains energy Irom the oxidation oI elemental sulIur. SulIuric acid is
produced. This bacterium thus can survive in extreme acidic environment.
S
0
H
2
O 1
1/2
O
2
--- H
2
SO
4
Energy
b) Oxidation oI H
2
S to S
Beggiatoa uses the energy Irom oxidation oI H
2
S Ior growth, and the product sulIur is stored as
granules in its Iilaments.
H
2
S O --- H
2
O S
0
Energy
3.4 Iron bacteria:
This is the most interesting and most simple oxidation, e.g, by Ferrobacillus. The Ferric ion is
deposited as insoluble Ierric hydroxide.
Fe
2
--- Fe
3
e
-


4. Chemosynthetic Heterotrophic Bacteria
This group is also known as Chemoorganotrophs; the organisms oI this group obtain energy Irom
oxidation-reduction reactions using organic compounds as the oxidizable substrate. Animals, Iungi
and most oI the bacteria (e.g. Escherichia coli) are chemoorganotrophs. The bacteria in this
category secrete extracellular enzymes which degrade complex nutrients, carbohydrates, proteins,
Iats etc. into simple smaller units which are absorbed and oxidized Ior release oI energy. II oxygen
serves as the uitimate hydrogen acceptor the energy yielding oxidation is called respiration; iI it is
an inorganic substance other than oxygen, it is called anaerobic respiration. It is called Iermentation
iI an organic substance serves as the hydrogen acceptor.

Microbial Fermentations
Fermentation is the process in which reducing equivalents are directly transIerred through the
coupling oI oxidation oI one substrate to the reduction oI a second substrate. The second substrate
is inIact oIten a product oI the catabolic pathway leading Irom the oxidized substrate, so such a
Iermentation pathway is internally balanced, with neither a net production nor a net requirement Ior
reducing equivalents. Fermentation mechanisms are Iound in the yeasts, and a number oI bacterial
groups and genera including the lactic acid and propionic acid bacteria, the Enterobacteriaceae,
Staphvlococcus, Bacillus and Clostridium spp.
The most important substrates oI the bacterial Iermentations are the carbohydrates. At least seven
distinct types oI Iermentation oI glucose are known, each having a diIIerent end product. Proteins
and amino acids are also Iermented. Much less is known about these Iermentations as compared to
glucose Iermentation. The bacteria are employed Ior the industrial production oI these products oI
Iermentation.

Microbial Respiration
In general, there are two mechanisms oI respiration viz. aerobic, and anaerobic. The
microorganisms have a varied ability oI a certain type oI respiration as described below:
1. Aerobic respiration
The respiration requiring the presence oI Iree oxygen in which glucose is completely oxidized to
CO
2
and H
2
O, is called aerobic respiration. Thus, in aerobes, O
2
serves the last Iunction. In other
words, the oxidation oI organic compounds by oxygen is called aerobic respiration; CO
2
H
2
O are
the end products. The role oI bacteria (as scavangers) in disposal oI organic debris is oI great
signiIicance. They are capable oI oxidizing any organic compound Iound in the living world. Most
oI the Iungi are strict aerobes.
2. Anaerobic respiration
It is the respiration in the absence oI Iree oxygen, in which glucose is partially oxidized. Here,
either an organic product oI metabolism or some inorganic substance replaces the O
2
. The ability to
grow non-phototrophically in the absence oI oxygen is conIined to certain bacterial, Iungal and
protozoal species. Bacteria oI the genus Desulfovibrio oxidize organic compounds anaerobically,
using sulphate as the hydrogen acceptor (oxidant). Another important anaerobic respiration
involves the use oI nitrate as hydrogen acceptor. It is reduced to N
2
or NH
3
by the denitriIying
bacteria. It is important to note that the sulIate reducers can not use oxygen even when available,
but the denitriIying bacteria use nitrates only in the absence oI oxygen. Among anaerobic bacteria,
the genus Clostridium is the most important.
3. Facultative anaerobic respiration
Certain species are classiIied as Iacultative anaerobes in that they are able to adapt their metabolism
to grow either in the presence oI oxygen or in its absence, other species are obligate anaerobes and
can only grow in an oxygen-Iree (anoxic) environment. Such organisms have the additional
problem that they are sensitive to an inhibitory or even lethal eIIect oI oxygen.

Chapter 4
MICROBIAL ECOLOGY

With the environmental awareness oI the 1970's, interest in natural science began to revive.
Suburban man has become acutely aware oI his environment, and there is new impetus to study the
natural world. The term ecology was coined by the German zoologist Ernst Haeckel, who called the
"relation oI the animal to its organic as well as its inorganic environment" kologie. The origin oI
the word is the Greek Oikos, meaning "household" or "home" or "place to live". Thus ecology deals
with the organism and its place to live. Basically this is the organism's environment; so ecology
might well be called environmental biology. The word environment covers a multitude oI things.
For one thing the environment includes the organisms's surroundings. It also includes Ior the
individual organism those oI its own kind, as well as organisms oI other kinds. There are
relationships between individuals within a population and with individuals oI diIIerent populations.
ThereIore, ecology reIers to the interrelations oI an organism with its environment and this includes
man also.
Because it deals with liIe, ecology has been considered a part oI biology. Earlier, the major
introductory path to biology was through natural history, or as it was more popularly known, nature
study. Modern ecology is Iocused upon the concept oI the Ecosystem, the major Iunctional unit
consisting oI interacting organisms and all aspects oI the environment. More technically, the
ecosystem is the selI-suIIicient habitat where living organisms and the nonliving environment
interact to exchange energy and matter in a continuing cycle. Starting Irom an individual we can go
upto several levels oI organization in ecology. The structure and physiology oI an individual has to
be studied in order to understand that how it is adapted to its environment. Then we come upto the
population level. A population is a group oI individuals in a given area or in a given locality.
Higher levels oI organization include the community which consists oI coexisting interdependent
populations and then the ecosystem or the community and its physical environment. Regional
ecosystems such as grassland and desert are called biomes. The largest biological system is the
biosphere or ecosphere which includes all the organisms living on carth interacting with the
physical environment.
Biosphere: It is the part oI earth in which the liIe exists. The entire world basically can be broadly
classiIied into abiotic and biotic components. Abiotic world is Iurther divided into atmosphere (air),
lithosphere (earth), and hydrosphere (water). To these three ecological components we can wind up
biological world that is biosphere. Thus a biosphere is the sum total oI atmosphere, hydrosphere
and lithosphere into which liIe penetrates.
Habitat: A habitat is a speciIic locality with particular set oI environmental conditions where
organisms live. Habitats are named aIter some prominent physical Ieature oI the environment or
dominant plant group e.g. stream habitat, Ireshwater habitat, rotten log habitat, and coniIerous
Iorest habitat. Thus the habitat oI Notonecta (black swimmer) is the shallow areas oI a pond which
is rich in vegetation, and the habitat oI a Irog is the damp shady places near water bodies. Habitat
may be as large as the ocean or as mall as the under-side oI a rotten log oI a tree, or the intestine oI
the termite. More than one animals or plants may live in a particular habitat.

THE ECOSYSTEM
A natural area, where living organisms and physical environment interact and exchange materials
between them so as to achieve Iunctional stability is known as ecosystem. An ecosystem may be
natural as a pond, a lake, a river, an ocean, a Iorest etc. or artiIicial like an aquarium, a dam or a
cropland. An ecosystem is never static as the organisms living in it are always interacting, not only
with one another but with the environment as well. II the environment aIIects and controls the
action oI organisms, then the organisms in return inIluence the non-living environment. This
reciprocal action is a common observation. For example, dissolved nutrients and oxygen in pond
water aIIect the growth oI the aquatic organisms that live there. The liIe activities oI these
organisms in turn modiIy these Iactors oI environment. The growth oI plants depletes the supply oI
nutrients. The respiration oI animals consumes oxygen and increases the amount oI carbon dioxide.
The most oI the ecosystems have the Iollowing characteristics.
1. Ecosystem is a major structural and Iunctional unit oI ecology.
2. The structure oI an ecosystem is related to the species diversity, a simple ecosystem has less
species diversity.
3. The Iunction oI the ecosystem is related to natural cycling oI nutrients and energy Ilow
through and within it.
4. Most ecosystems mature by passing Irom less complex to more complex state.
The Iundamental steps in the operation oI an ecosystem are:
1. Production oI organic material by producers.
2. Consumption oI this material by consumers and its Iurther elaboraiion.
3. Decomposition oI inorganic compounds, and
4. TransIormation to Iorms suitable Ior the nutrition oI producers.
Components of the Ecosystem
Each ecosystem has its own unique combination oI living organisms (biotic component) and abiotic
resources that Iunction to maintain a continuous Ilow oI energy and nutrients (Figure 4.1).
All ecosystems have two types oI organisms based on carbon source. Autotrophs use inorganic
carbon and are the producers. Heterotrophs use organic carbon and are the consumers and
decomposers. The sun is the major source oI energy to run the system.


Figure 4.1: Major components of a self-sufficient ecosystem.


AGROECOSYSTEM
Agroecosystems contain less diversity oI animal and plant species than natural ecosystems. Usually
there are a Iew major species, and numerous minor species. The agroecosystem is intensively
manipulated by man and subjected to sudden alteration such as plowing, mowing and treatments oI
Iertilizers and pesticides. Thus agroecosystems can be more susceptible to pest damage and other
clamaties because oI the lack oI diversity in species oI plants, insects and microorganisms, and a
sudden alteration imposed by weather or man. The agroecosystem is not stable.

Agroecosystems that Stimulate Natural Ecosystems
When plants and animals in a natural ecosystem which have little or no agricultural use are
replaced by similar plants and animals which are more useIul in agricultural terms, the result is an
agroecosystem.
Where ecological and economic conditions are Iavourable (e.g. Ilat, Iertile land; high market
demand, availability oI artiIicial inputs), a Iarm system with less perennial biomass (trees, shrubs,
grasses, animals) and Iunctional diversity than the natural ecosystem may be preIerable Irom a
production-oriented point oI view. Under low external input agriculture conditions, where diverse
products are needed and where perennial biomass and Iunctional diversity are oI key importance
Ior protecting and reproducing the Iarm system, agroecosystems would ideally approach the climax
ecosystem Ior the site. In the tropics, this would normally be same type oI agroIorestry system; in
drier area, savanna-like systems with scattered trees, shrubs and perennial grasses; and in more
humid areas, systems which resemble more dense Iorest.
The characteristics oI natural ecosystems can be used as the basis Ior designing sustainable Iarm
systems. For example, the ideal agroIorestry system is designed to imitate the ways in which
natural ecosystems save or accumulate nutrients against the Iorces oI erosion, Iire, leaching and
volatilization and, thus, ensure a continuous turnover oI biomass. The natural mechanisms oI
nutrient accumulation are (Woudmansee, 1984):
1. Continuous vegetation cover,
2. litter layer on the soil,
3. synchronized plant and microbial activities,
4. retention oI large portion oI ecosystem nutrients in living tissues, particularly in wetland
systems, and
5. broad heterogeneity in rooting structures.
Hart (1980) has suggested an analogue approach to designing sequential Iood production systems:
managing a Iarm site so as to imitate natural succession.
Beginning with annual grasses and broadleaved species such as maize and beans, the system
progresses through stages oI planting to a 'Iorest' oI economically valuable trees and understorey
crops with many oI ecological characteristics oI a maturing tropical rainIorest. The highly diverse
and productive home gardens oI Java and Sri Lanka exempliIy traditional systems that simulate
natural succession: each stage creates the physical conditions (light/shade, soil organic matter etc.)
needed by the next. Directing succession rather than Iighting it reduces the battle against weeds
characteristic oI annual cropping systems, lowers the energy and labour costs oI establishing
perennial crops, and results in an evolving Iarm system with increasing diversity and reduced
susceptibility to disruption (Dover and Talbot, 1987). Indigenous agriculture presents many
examples oI close simulation oI natural ecosystems. These could be used as a basis Ior developing
Iarm systems which combine optimal use oI local resources with judicious use oI ext.ernal inputs.
Status of Microorganisms in the Ecosystem
LiIe within the soil is analogous to liIe above the soil. Roots, tubers, and other underground plants
are parts oI primary producers. There are consumers and decomposers interrelated by Iood chains.
Perhaps the major diIIerence between the ecology above and below the soil-atmosphere interIace is
that above the interIace animals play the dominant role as consumers, and below the interIace
microorganisms play the dominant role as decomposers. Dead bodies oI plants and heterotrophic
organisms are decomposed by microorganisms and thus nutrients are released in the environment.
These nutrients are used by plants in their growth which in turn Iorm Iood Ior the heterotrophic
organisms. These back and Iorth movements oI chemical elements between organisms and
environment along characteristics circular paths are known as biogeochemical cycles e.g.
Carbon-Hydrogen-Oxygen cycle, Nitrogen cycle etc.; and the microorganisms play an important
role as the ultimate decomposers. There are so many processes other than organic matter
decomposition that the microorganisms perIorm in the ecosystem, e.g. atmospheric N-Iixation,
P-solubilization, biological pest control, Iermentations in the Iood and beverage industry,
antibiotics production Ior the control oI diseases in animals and human beings, Iood digestion in the
ruminants, degradation oI toxic chemicals in the soil etc.

MICROBES AND THE ENVIRONMENT
The study oI microbial ecology requires consideration oI organisms, biological processes, and the
spatial and dynamic aspects oI soil micro environments and microhabitats. The latter are a
consequence oI climatic inIluences on parent material and topography with time. Basic to all
terrestrial ecosystems is soil. Populated by high numbers oI species as well as individuals, the soil
embraces another world with its whole chain oI liIe, its predators and prey, its herbivores and
carnivores, and its Iluctuating populations. Because oI their abundance, Ieeding habits, and ways oI
liIe, these small organisms have an important inIluence on the world a Iew inches above them.
Because Ior all practical purposes it is a community separate Irom the one above, soil has been
considered ecosystem or biocenoses, but it is not. Its energy source comes Irom dead bodies and
Ieces Irom the community above. It is but a stratum oI the whole ecosystem oI which it is a part.
The soil is a radically diIIerent environment Ior liIe than the one above the surIace, yet the essential
requirements do not diIIer. Like animals that live outside the soil, soil Iauna require living space,
oxygen, Iood and water.
The microorganisms have been divided into two groups according to their relation with the
environment and survival strategies, These are:
Autochthonous (permanent or indigenous):
These are original microbes oI an ecosystem, also called as true residents. They participate in
community activity; and they Ilourish dramatically and decline shortly when organic matter gets
short. However, they are permanent members oI the microbial community.
Allochthonous (transient or invadors):
They do not participate in the community activities; and they grow slowly and persist more.
Environmental conditions aIIect the density and composition oI microbes. Various Iactors aIIecting
are: moisture, aeration, the temperature, organic matter, acidity, and inorganic nutrients supply.
Moisture being major component oI protoplasm, it must be adequate Ior vegetative development.
Excessive moisture creates aeration problem and lowers the available oxygen supply. Optimum
level Ior aerobic bacteria is 50-70 oI moisture holding capacity oI the medium. Waterlogging
brings a decrease in the number oI aerobes, and encouragement oI anaerobes. According to
temperature demands, three microbial groups are recognized: Psychrophiles which develop best at
lower temperature less than 20C. They are most common in the nature. Mesophile most abundant at
an optimum range oI temperature viz. 25-35C. Thermophiles grow readily at higher temperature
range Irom 45-65C. Temperature also aIIects the biochemical changes brought about by the
microbes. Warming trends will Iavor the biochemical changes. Humus rich locality has the largest
microbial number. By addition oI the organic matter in the soil, the number oI microbes in soil will
increase. The hydrogen ion concentration optimum Ior microbial growth is near neutrality. Some
bacteria may, however, stay at pH 3. In addition to organic carbon, inorganic nutrients are also
required Ior the growth oI microorganisms.
Many microorganisms exhibit a range oI phenotypes in response to diIIerent environmental
conditions and which, in some cases, may result in the expression oI a number oI completely
diIIerent morphological Iorms. This has also led to the erroneous identiIication oI a number oI
diIIerent 'species'. The microbial ecologist is only just beginning to explore quantitatively the
potential oI diIIerent growth systems in examining this area oI microbial ecology. It is also now
well established that the growth environment inIluences the expression oI such cellular components
as enzymes and aIIects their leveis and activities (Clarke and Lilly, 1969). Furthermore, it has
recently been shown that more than one pathway may exist in the same organism, capable oI
IulIilling the same metabolic Iunction and which mechanism operates depends on the growth
environment oI the organism.
Microbial Populations and Communities
In the past much emphasis has been placed on understanding the growth oI populations containing
single species oI microorganism. It is, however, obvious that in nature populations oI
microorganisms do not oIten grow in complete isolation Irom each other and that, as a result, a
variety oI interactions exist between the diIIerent populations (Slater, 1978; Slater and Bull, 1978).
Competition is one oI the more important interactions together with prey-predator relationships.
Furthermore, it is now well established that stable associations oI microorganisms, termed
microbial communities also occur in nature (Senior et al., 1976; Slater, 1978).
The Iormation oI microbial ecosystem is governed by the biological equilibrium generated by the
interactions and associations oI all the organisms Iound in the populations. There are certain types
oI interactions possible between two species or organisms. All types oI interactions are termed as
symbioses, whether they be inconsequential, advantageous, or detrimental Ior either, neither, or
both (or more) interacting partners or populations. In the Iollowings terms have been deIined Ior
various neutral, positive, and negative interactions. The terminology is useIul, inspite oI the Iact
that interactions in nature will normally involve more than two populations interacting
simultaneously and sequentially (Stotzky, 1972).

1. Neutral Interactions
1.1 Neutralism:
The condition in which two microorganisms or populations behave entirely independently, and they
have neither a positive nor negative inIluence on each other under any circumstance. Neutralism is
probably uncommon, because microorganisms alter the environment (e.g. as a consequence oI
changing the ratios oI gases in the soil atmosphere, pH, Eh etc.).

2. Positive Interactions
2.1 Commensalism:
A relationship in which one organism is dependent upon production by another organism oI a
growth Iactor, such as vitamin. In the absence oI the provider the auxotroph suIIers, whereas the
vitamin synthesizer neither suIIers nor beneIits by the presence or absence oI its dependent.
Another example oI commensalism is the degradation by one species oI a compound toxic to a host
oI other species otherwise unable to proliIerate in a given micro habitat (Stotzky, 1972).
2.2 Protocooperation:
It is a non obligatory but potentially beneIicial relationship Ior both participants. For examples, the
relation between Iree-living N-Iixing bacteria and non Iixers. The diazotroph enriches micro
habitats with available N, there by permitting increased activity by non Iixers which in turn, supply
elevated levels oI the required energy-rich, readily utilizable C-compounds to support N-Iixation.
The crop residue systems in which degradation oI cellulosic and other N-poor substrates is
supported by protocooperative N-Iixation. Protocooperation also extends to many symbioses
commonly, but less correctly, reIerred to as mutualism. Syntrophic associations in which two or
more species or strains are required Ior the complementary exploitation oI resources, also come
under this category.
3. Negative Interactions
Negative interactions between and among microorganisms are probably more common than
positive, and perhaps the most common Iorm oI negative interaction is competition Ior limited
resources (Stotzky, 1972).
3.1 Competition:
This is a state in which one species is suppressed as the two or more species struggle Ior limited
supply oI nutrients, oxygen, carbon or other requirements Ior their existence. Competition oI C and
energy sources is probably the most prevalent, but competition Ior mineral nutrients, water,
terminal election acceptor (O
2
and NO
3
-
), and space can also occur when these are limiting.
3.2 Amensalism:
A situation in which one species is Iavoured by its ability to export metabolites (toxins) that
adversely aIIect other species, with the result that one species is suppressed while the second is not
aIIected. The result oI an amensal interaction can be direct, as with in situ antibiotic and organic or
inorganic inhibitor production (Thomashow and Weller, 1991) or indirect, as when the metabolitic
activities oI one group oI microbes results in alteration oI microenvironmental conditions (pH, Eh,
soil atmosphere etc.) to be detrimental Ior another.
3.3 Parasitism and Predation:
These are the direct attack oI one organism on another i.e. negative interaction in which one
population directly exploits another as a Iood source. By strict deIinition, these are obligate
interactions Ior the predator or parasite. However, examples are known oI microbes that are
Iacultative predators or opportunistic parasites. For example, opportunistic Iungal and bacterial root
pathogens, the principal nutritional mode oI which is saprophytic, are, on the other hand, quite
common and are responsible Ior signiIicant economic loss to what Cook and Baker (1983) reIer to
as subclinical pathogenesis. Similarly the noval bacterium Cupriavidus, has simple nutritive
requirements, but it is also capable oI switching to a predatory mode at the expense oI several gram
ve and gram -ve bacteria when simple carbonaceous substrates are limiting (Makkar and Casida,
1987).
OI course, microbial community dynamics seldom reIlect simple positive or negative interactions.
Rather, at any given time, the direction oI change within a microhabitat is the sum total oI many
interactions set in motion with provision oI a utilizable nutrient source and the absence oI
microenvironmental extremes (Metting, 1993). A good example is the combination oI syntrophic,
competitive, and amensal interaction typical oI a microhabitat under Iermentative conditions.
Chapter 5

THE EFFECTIVE MICROORGANISMS

There has been an extraordinary increase in interest and activity on the subject oI biotechnology in
the last Iew years. The biotechnology can be best deIined as the industrial exploitation oI biological
systems or processes, and it is largely based upon the expertise oI biological systems in recognition
and catalysis. The EM-Technology is one oI the biotechnologies used in agricultural production.
Biotechnological practices can provide routes to the improvement oI whole crops, both in terms oI
quality and yield. It can provide supplements or alternatives to expensive and environmentally
hazardous chemical Iertilizers and pesticides. Biotechnology and agriculture interact in many ways,
thereIore, the agriculture can be revolutionized by the application oI biological principles and
materials. The EM-Technology can be deIined as Iarming with the use oI EIIective Microorganisms
(EM) alone or alongwith some organic materials in order to provide the necessary nutrients and to
control the diseases and pests oI crops and Iarm animals eIIiciently. The EM technology is
economically and environmentally sound method oI Iarming.
The term EM does not mean a speciIic microorganism rather it is a large group oI co-existing
microorganisms in a culture solution which have a broad-spectrum eIIect on crop and livestock
production. The EM includes photosynthetic N-Iixing and lactic acid producing bacertia, yeasts,
molds and ray Iungi making a total oI 10 genera and 80 species. The main eIIects oI EM are to Iix
atmospheric nitrogen, solubilize the unavailable nutrients, develop organic matter in the soil
through photosynthesis, improve the physical properties oI soil, control the diseases by producing
lactic acid and other antibiotics, decompose organic matter in the soil, degrade the animal Ieed to
make it more digestible, remove the malodours Irom the animal sheds/manures and so on. Although
all these mechanisms have already been discovered by other scientists, but their approach was
solitary i.e. they studied the eIIect oI single species oI microbes on any one oI the above mentioned
processes. Whereas the discovery oI EM has made it possible and easier to tackle a number oI
problems with a single mixture oI microorganisms i.e. many in one. Now the utilization oI EM is
widespread in a number oI countries on various aspects.
The EM Technology is the latest approach in nature Iarming that is now applicable to IulIill the
needs oI increasing population without using chemical inputs. Most recently, this type oI
technology was introduced in China under the name oI Yield Increasing Bacteria (YIB) as reported
by Chen et al. (unpublished) in a paper. On an average 10-15 increase in the yield oI various Iield
crops due to plant growth promoting substances, was observed with YIB application, however,
disease incidence was controlled mostly Irom 50-70 on various crops by biological control
mechanisms. These Iindings provide a prooI oI beneIicial eIIects oI mixed microbial cultures on the
crop production.
BeIore it is actually disclosed the exact composition oI the EM culture, it would be beneIicial Ior
the readers and the researchers to get an idea oI the beneIicial eIIects oI various species oI microbes
as reported by various scientists. In the Iollowings a comprehensive review pertaining to various
categories oI beneIits oI microorganisms is given, so that the philosophy oI EM could be
understood.
Biological N-Fixation
Symbiotic nitrogen Iixation by Rhi:obium bacteria in the leguminous plants is well documented
and also a lot oI research work has proved atmospheric N-Iixation by Iree-living microorganisms.
The Iree-living bacteria having the ability to Iix atmospheric nitrogen can be distinguished into
obligate aerobic, Iacultative aerobic and anaerobic organisms. Obligate aerobic bacteria belong to
the genera A:otobacter, Beiferinckia, Derxia, Archromobacter, Mvcobacterium, Arthrobacter and
Bacillus. Among the Iacultative anaerobic bacteria are the genera Aerobacter, Klebsiella and
Pseudomonas. Anaerobic N-Iixing bacteria are represented by the genera Clostridium, Chlorobium,
Chromatium, Rhodomicrobium, Rhodopseudomonas, Rhodospirillum, Desulfovibrio and
Methanobacterium. In some oI these genera, N-Iixation takes place in photoautotrophic manner
exampliIied by genus Rhodopseudomonas. While the genus DesulIovibrio Iixes nitrogen in the
process oI reducing sulphates.
Other than bacteria, there are certain other microbes viz. actinomycetes and blue-green algae that
have the ability to Iix atmospheric nitrogen. The blue-green algae comprise unicellular, colonial
and Iilamentous types. Most oI the blue-green algae belong to the orders Nostocales and
Stigonematales under the genera Anabaena, Anabaenopsis, Aulosira, Chlorogloea,
Cvlindrospermum, Nostoc, Calothrix, Scvtonema, Tolvpothrix, Fischerella, Hapalosiphon,
Mastigocladus, Stigonema and Westiellopsis. In pure cultures, BGA can Iix nitrogen Irom 5.2 to
14.48 mg/100 ml oI the medium. There are some blue-green algae which exist in association with
Iungi, liverworts, Ierns and Ilowering plants. For example, the association oI BGA with a water
Iern A:olla is being used as green compost Ior rice cultivation Irom which more than 100 kg N ha
-1

can be obtained. Actinomycetes e.g. Frankia is know to Iix nitrogen in Alnus. Similarly, about 17
genera oI angiosperms oI worldwide distribution possess root nodules as in the leguminous trees.
LeaI nodules have also been Iound in the Iamilies oI Rubiaceae and Myrsinaceae.
Phosphorus Solubilization
The availability oI phosphorus to plants is a widespread problem as it is Iixed in acidic as well as
alkaline soils by making insoluble compounds with Fe and Ca, respectively. A bacterium Bacillus
megatherium var. phosphalicum is known to solubilize the precipitated phosphorus compounds. In
another way, Iungal association with plant roots by VA mycorrhizae, exists which extends the root
area Ior direct contact to soil phosphorus. In this way uptake oI phosphorus by plants is enhanced.
There are two types oI mycorrhizae- ecto and endo mycorrhizae. Ectomycorrhizae are known to
occur in the Iollowing Iamilies: Pinaceae, Salicaceae, Betulaceae, Fagaceae, Juglandaceae,
Ceasalpinoideae and Tiliaceae. The Iungi involved in ectomycorrhizae belong to the genera-
Amanita, Boletus, Cantharellus, Cortinarius, Entoloma, Gomphidium, Hebeloma, Inocvbe,
Lactarius, Paxillus, Russula, Rhi:opogon, Scleroderma and Cenococcum. Many oI these Iungi
show a wide host spectrum. The Iungi involved in endotrophic association belong either to the
Phycomycetes or to the Basidiomycetes. One group oI orchid mycorrhizal Iungi belonging to
Basidiomycetes including the genera Armillaria, Fomes, Zerotus, Corticium and Marasmium. The
other group belongs to Fungi ImperIecti under the genus Rhi:octonia.
Organic Matter Decomposition
The organic compounds are made up oI complex carbohydrates, simple sugars, starch, cellulose,
hemicelluloses, pectins, gums, mucilage, proteins, Iats, oils, waxes, resins, alcohols, aldehydes,
ketones, organic acids, lignins, phenols, tannins, hydrocarbons, alkaloids, pigments and other
products. The size oI particles in the organic matter, the nature and abundance oI microorganisms
involved, the extent oI availability oI C, N, P and K, the moisture content, temperature, pH,
aeration, and presence oI inhibitory substanbes (such as tannins) etc. are some oI the major Iactors
which inIluence the rate oI organic matter decomposition. The genera oI the microorganisms taking
part in the decomposition oI organic matter are enlisted in Table 5.1. These microorganisms can be
Iurther grouped into aerobic and anaerobic debomposers.
Plant Growth Promoting Substances
Microorganisms produce a variety oI substances which directly or indirectly aIIect plant growth.
Some oI the most important microbial products capable oI inIluencing the development oI plants
are indole acetic acid (IAA), giberellins, antibiotics, cytokinins and ethylene etc.
Many species oI bacteria and Iungi are capable oI producing IAA in small amounts especially when
the growth medium is supplemented with a precursor tryptophane. The microbes include
Agrobacterium tumefaciens, Ustilago mavdis, Svnchvtrium endobioticum, Gvmnosporangium
funiperi-virginianae, Nectria galligena, Endophvllum sempervivi, Rhi:obium spp., Rhi:opus suinus
and Pseudomonas flourescens.


Table 5.1: Genera of microorganisms capable of utilising different components of organic
matter as reported by several worker: F-fungi; B-bacteria; A-actinomycetes: (N.S. Subba Rao,
1986)
Nature oI
substrate in
organic matter
Genera oI microorganisms

F: Alternaria, Aspergillus, Chaetomium, Coprinus, Fomes, Fusarium,
Mvrothecium, Penicillium, Polvporus, Rhi:octonia, Rhi:opus, Trametes,
Trichoderma, Trichothecium, Jerticillium, Zvgorvnchus.
B: Achromobacter, Angiococcus, Bacillus, Cellfalcicula, Cellulomonas,
Cellvibrio, Clostridium, Cvtophaga, Polvangium, Pseudomonas, Sorangium,
Sporocvtophaga. Jibrio
Cellulose
A: Mcromonospora, Nocardia, Streptomvces, Streptosporangium.
F: Alternaria, Fusarium, Trichothecium, Aspergillus, Rhi:opus, Zvgorvnchus,
Chaetomium, Helminthosporium, Penicillium, Coriolus, Fomes, Polvporus.
B: Bacillus, Achromobacter, Pseudomonas, Cvtophaga, Sporocvtophaga,
Lactobacillus, Jibrio.
Hemicellulose
A: Streptomvces.
F: Clavaria, Clitocvbe, Collvbia, Flammula Hvpholoma, Lepiota, Mvcena,
Pholiota, Arthrobotlvs, Cephalosporium, Humicola.
Lignin
B: Pseudomona, Flavobacterium.
F: Aspergillus, Fomes, Fusarium, Polvporms, Rhi:opus.
B: Achromobacter, Bacillus, Chromobacterium, Clostriclium, Cvtophaga.
Starch
A: Micromonospora, Nocardia, Streptomvces.
F: Fusarium, Jerticillium. Pectin
B: Bacillus, Clostridium, Pseudomonas.
F: Penicillium, Aspergillus, Fusarium. Inulin
B: Pseudomonas, Flavobacterium, Benechea, Micrococcus, Cvtophaga,
Clostridium.
F: Fusarium, Mucor, Mortierella, Trichoderma, Aspergillus, Gliocladium,
Penicillium Thamnidium, Absidia.
B: Cvtophaga, Achromobacter, Bacillus, Beneckea, Chromobacterium,
Flavobacterium, Micrococcus, Pseudomonas.
Chitin
A: Streptomvces, Nocardia, Micromonospora.
B: Bacillus, Pseudomonas, Clostridium, Serratia, Micrococcus. Proteins and
nucleic acids
F: Penicillium, Rhodotorula, Mortierella.
B: Bacillus Cutin
A: Streptomvces
Tannin F: Aspergillus, Penicillium
Humic acid F: Penicillium, Polvstictus
Fulvic acid F: Poria

The gibbereellins are produced by the bacteria A:otobacter, A:ospirillum, Arthrobacter, Bacillus,
Brevibacterium, Pseudomonas, Rhi:obium, Actinomvcetes belonging to Actinomvces, Nocardia,
Streptomvces; and the Iungi Alternaria, Aspergillus, Fusarium, Gibberella fufikuroi, Penicillium,
Rhi:opus, Rhi:opogon, Sphaceloma etc. Some oI gibberellin are known to be natural components
oI plants controlling their growth activities, dormancy, Ilowering and responses to light and
temperature. Some gibberellins can do the Iollowings:
1. Overcome dormancy and dwarIism in plants,
2. they induce Ilowering oI some photoperiodically sensitive and other low temperature
dependent plants,
3. they alter the sex oI Ilowers and contribute to Iruit setting, and
4. they stimulate stem growth and at the same time suppress the growth oI latteral branches.
Cytokinins are also plant growth regulators that can be produced by rhizosphere microbes. The
bacteria which are able to produce these metabolites include A:otobacter, A:ospirillum,
Arthrobacter, Agrobacterium, Bacillus, Corvneform, Corvnebacterium, Escherichia, Pseudomonas;
and the Iungi possessing this ability are, Amanita, Boletus, Dictvostelium, Exobasidium, Glomus,
Monilia, Nectria, Rhi:opogon, Suillus, Taphrina. Among the actinomycetes, the Actinomvces,
Frankia, Nocardia and Streptomvces can produce cytokinins.
Ethylenes are produced by the bacteria Aeromonas, Arthrobacter, Clostridium, Citrobacter,
Pseudomonas, Enterobactor, Escherichia, Klebsiella, Serratia; while the Iungi involved are
Agricus, Alternaria, Aspergillus, Fusarium, Mucor, Penicillium, Rhi:opus; and the actinomycetes
having this property are Actinomvces, Frankia, Nocardia and Streptomvces.
Biological Pest Control
There are a number oI bacteria and Iungi that control the diseases and pests oI plants and animals
by producing antibiotics and other compounds toxic to the pests, and also by direct parasitism on
the insect/pests. For example, the antiIungal antibiotics produced by Penicillium griseofulvum, and
Streptoverticillium cinnamomeum var. terricolum. Hundreds oI similar microbes are capable to
produce antibiotics. In Japan, agriculturally useIul antibiotics have been used to protect plants
against diseases and pests. There are about 90 species oI bacteria pathogenic to insect pests, among
them Bacillus thuringiensis stands out prominent. Other insect pathogens are Bacillus popilliae,
Coccobacillus acridorum and Serratia marcescens. Fungi includes Entomophthora spp., Beauveria
spp., Metarrhi:ium anisopliae and Aeschersonia spp. There are also known more than 300 viruses
which rapidly inIect susceptible species oI insects.
Microbial Herbicides
The concept oI herbicides oI microbial origin is credited to plant pathologists who use endemic or
exotic pathogens to kill weeds. For example, the use oI Puccinia chondrillina to control skeleton
weed, the use oI Cercosporella riparia to control Ageralina riparia, and the use oI introduced rust
Phragmidium violaceum to control wild blackberry. Similarly, some oI the successes with endemic
pathogens are also quoted in the literature.
Silage Making with Microbes
A considerable research has been carried out to improve our understanding oI the microbiological
and biochemical changes which occur during the conservation oI grass as silage. Some species oI
lactic acid bacteria viz. Lactobacillus and Streptococcus are capable oI Iermentation oI the grass to
silage. Studies on a wide range oI silages indicate that the digestibility oI well preserved (lactate
dominant) silages is similar to that oI the original grass.
Intestinal Microbes in Animal
The digestibility oI various Iorage celluloses and hemicelluloses by ruminants and non-ruminants
rarely exceeds 50, thus the remaining is lost. By making the intestinal Iermentating microbes
eIIicient, this wasted Iood can be converted into calories. A similar Iermentative process occurs
with starch and sugars. The inIluence upon the ruminant's vitamin economy is oI outstanding
importance, since the synthetic abilities oI the microbial population provide the host animal with a
complete supply oI the B-vitamins. ThereIore, the cellulolytic and lignolytic microbes introduced
into the animals digestive system may play an important role in the improvement oI animal
nutrition.
Pollution Control through Microbes
There are some bacteria which degrade the toxic chemicals in the soil and also in the composts,
very eIIiciently, so that their residues may not harm the human beings. These bacteria and Iungi are
very important in the degradation oI pesticides. For example, the microorganisms known to
metabolize DDT to DDD are, Achromobacter, Aerobacter, Agrobacterium, Bacillus, Clostridium.
Corvnebacterium, Escherichia, Erwinia, Kurthia, Pseudomonas and Streptococcus. Similarly,
Aldrin is converted to Dialdrin by Trichoderma, Fusarium, Penecillium, and Pseudomonas without
any loss oI insecticidal property. Many other microbes are known to degrade herbicides, Iungicides
and other toxic compounds in the soil.
The Composition of Effective Microorganisms
From the review oI previous mechanisms controlled by microorganisms it is now easy to
understand that how it is possible to achieve a number oI beneIits Irom a single solution oI
microorganisms. As described earlier, that EM is composed oI 80 species oI microbes coexisting in
a culture solution. Technically, it is very diIIicult to culture such a large number oI beneIicial
microbes in a single media while every microbe has its own living requirement, and there also exist
a number oI Iactors like antagonism, aIIecting the existence oI these microbes. Doesn't matter, a
well understanding oI the microbial ecology can make it possible to adjust the requirements oI each
microorganism by joining with the other one. For example, one microbe produces the compounds
to be used Ior the other. Similarly, nutritional and other requirements like oxygen, are linked in a
type oI Iood-web, or cycle oI events, so that all the microorganisms live together without harming
each other. Thus the cumulative or even selective eIIect where whatever needed can be got Irom a
single solution.
The EM have been divided into many groups like, aerobic N-Iixer, anaerobic N-Iixer,
photosynthetic N-Iixer, organic matter decomposers, lactic acid producing, antibiotics producing,
nutrients solubilizing, and growth promoting substances producing microbes. The detail oI the
genera/species in each group oI EM is given in the Iollowings:

(The remaining portion oI this chapter will be included in the next edition aIter getting permission
Irom Dr.Teruo Higa, and INFRC, Japan)
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