SOIL MICROBIOLOGY AND PLANT PATHOLOGY
BIO 3205:
NAME OF PROGRAMME
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BACHELOR OF SCIENCE EDUCATION
COURSE TITLE
COURSE CODE
:
:
SOIL MICROBIOLOGY AND PLANT PATHOLOGY
BIO 3205
Course Description:
Soil is the “PLACENTA” of life, therefore activities of organisms living in soil affect the welfare of
crop plants growing rooted in soil. The pathogenic fungi and diseases they cause will be studied and
methods of disease control discussed.
Objectives of the course
At the end of the course the students should be able to;
 Recognize crop plants with disease symptoms.
 Isolate bacteria and fungi from infected plants.
 Identify the pathogens.
 Suggest methods of control of the disease.
EXPECTED OUTCOMES
Graduates with competence to recognize and deal with serious crop diseases.
YEAR WHEN OFFERED
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COURSE DURATION (CONTACT HOURS) :
CREDIT UNITS
Year Three, Semester Two
45 Hour
:
Three
METHOD(S) OF DELIVERY
 Lectures
 Laboratory work examining specimens and performing experiments
 Essay writing assignments
METHODS OF ASSESSMENT
 Class tests
 Assignments
 University exams
AVAILABLE RESOURCES
 Teaching rooms and laboratory
 Library
 Laboratory equipment
Detailed course content
1.
2.
Soil microbiology:

The soil profile

Biotic and abiotic components of soil

Fungal structures found in soil

Colonization and exploitation of “DEAD” substrata by fungi in soil.

Bacteria in soil

Living plant roots and soil microbiota

Factors affecting the nature of Rhizosphere and root surface microbiota.

Effects of soil micro-organisms on plant life,
5 Hrs
10 PH
Plant pathology:

Definition of plant pathology

Causes of diseases of plants
5 Hrs

How plant pathogens enter their hosts
2 PH

How plant pathogens induce disease in their hosts.

How plant disease epidemics develop and how they decline.

How plants defend themselves against plant diseases.
TO BE TREATED IN FAIR
DETAIL:
LOCAL AND INTERNATIONAL PLANT DISEASES
(i)
(ii)
Diseases of the root system:

Diseases of germinating seeds and seedlings
4 Hrs

Root rots
2 PH

Specialized soil parasites
Diseases of the shoot system:

Blights

Vascular wilts
11 Hrs

Soft rots

Mildews

Rusts

Smuts
10 PH
Methods of control of plant disease
3 Hrs
6 PH
Suggested reading list
1. David H. Thurston (2000). Tropical Plant Diseases 2nd Edition. APS Press
2.
Hill, D.S and Waller J., (1990) Pests and Diseases of Tropical Crops – Field Handbook – Produced by Longmans Camp
(F.E) LTD.
3.
Tushemereirwe, W.K et all (2003) BANANA PRODUCTION MANUAL: A guide to successful Banana Production in
Uganda. Kawanda Agricultural Research Institute.
4.
Acland, J.O (1973) East African Crops. Longman Group Limited.
5.
Burchill, R.T Ed (1981) Methods In Plant Pathology. Commonwealth Mycological Institute Phytopathogical Paper No.
26.
6.
Bradbury, J.F (1970) Isolation and Preliminary Study of bacteria from plants. Review of Plant Pathology 49.
Topic One
Soil microbiology
Soil microbiology is the study of organisms in soil, their functions, and how they affect soil properties.
Soil microbiology is the scientific discipline that is concerned with the study of all biological aspects
of the life that exist in the soil environment. Microorganisms in soil are important because they affect
soil structure and fertility. Soil is an excellent culture media for the growth and development of various
microorganisms. Living organisms present in the soil are grouped into two categories as Soil and Soil
fauna. Soil is not a static material but a medium with life. Soil is now believed to be dynamic or a
living system. Soil provides shelters for many animal types, from micro-organisms, invertebrates such
as worms and insects up to mammals like rabbits, moles, foxes and badgers.
The soil is not a mass of dead debris, it results from physical and chemical weathering of rocks; it is a
more or less homogeneous system which has resulted from the decomposition of plant and animal
remains. A normal soil is made up of solid, liquid, and gaseous constituents. These can be broadly
divided into five groups:
1. Mineral Particles. 2. Plant and Animal Residues. 3. Living Systems. 4. Water. and 5. Gases.
There are millions and billions of microbial cells per gram, depending upon soil fertility and the
environment. Dead vegetation, human and animal wastes, and dead animals are deposited in or on soil.
In time they all decompose into substances that contribute to soil, and microbes are largely responsible
for these transformations. Distribution of Microorganisms in soils is an important aspect in soil studies.
Microorganisms constitute < 0.5% (w/w) of the soil mass, yet they have a major impact on soil
properties and processes. About 60-80 % of the total soil metabolism is due to the microflora. These
are the smallest organisms (<0.1 mm in diameter) and are extremely abundant and diverse.
Two great pioneer soil microbiologists were Martinus W. Beijerinck (1851–1931), a Dutchman, and
Sergey N. Winogradsky (1856–1953), a Russian. These researchers isolated and identified new types
of bacteria from soil, particularly autotrophic bacteria, that use inorganic chemicals as nutrients and as
a source of energy. The relationship between legumes and bacteria in the nodules of legume roots was
discovered by other scientists in 1888. The nodules contain large numbers of bacteria (Rhizobium) that
are capable of fixing atmospheric nitrogen into compounds that can be used by plants.
The ecology of fertile soil consists of plant roots, animals such as rodents, insects, and worms, and
a composite of microorganisms—viruses, bacteria, algae, fungi, and protozoa. The role of this
microbial flora can be conveniently expressed in Earth’s natural cycles. In the nitrogen cycle, for
example, microorganisms capture nitrogen gas from the atmosphere and convert it into a combined
form of nitrogen that plants can use as a nutrient; the plant synthesizes organic nitrogen compounds that
are consumed by humans and animals; the consumed nitrogen compounds eventually reach the soil;
microorganisms complete the cycle by decomposing these compounds back to atmospheric nitrogen
and simple inorganic molecules that can be used by plants. In similar cycles for other elements such as
carbon, sulfur, and phosphorus, microbes play a role; this makes them essential in the maintaining of
life on Earth.
Importance of Soil Organisms
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Responsible for cycling of C, N and other nutrients
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Enhance soil structure
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Relocate and decompose organic materials
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Maintain soil quality and health
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Increase soil aeration and penetrability
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Involved in disease transmission and control
The activity of living organisms in soil helps to control its quality, depth, structure and properties. The
climate, slope, locale and bedrock also contribute to the nature of soil in different locations. The
interactions between these multiple factors are responsible for the variation of soil types.
Plants are the major producers of organic material to be found in soil, and plant matter accumulates as
litter. Animal faeces and the decomposing bodies of dead animals complement this organic supply.
Artificially added fertilisers, herbicides and pesticides all affect the biological component and hence
the organic content of soils. Animal droppings/dung and chicken manure are beloved of gardeners.
Microbes play a central role in re-cycling such material. Besides recycling of naturally occurring
organic compounds, soil microbes are responsible for the chemical degradation of pesticides.
Organic matter affects both the chemical and physical properties of the soil and its overall health.
Properties influenced by organic matter include: soil structure; moisture holding capacity; diversity
and activity of soil organisms, both those that are beneficial and harmful to crop production;
and nutrient availability. It also influences the effects of chemical amendments, fertilizers, pesticides
and herbicides.
Plant pathology
Plants are subject to infection by thousands of species of very diverse organisms, most of which are
microbes. These disease-producing plant pathogens cause significant agricultural losses and include
viruses, bacteria, and mycoplasma-like organisms and fungi. The study of plant diseases is called plant
pathology.
The soil profile
The soil profile is a vertical section of the soil that depicts all of its horizons. The soil profile extends
from the soil surface to the parent rock material.
The soil profile can be diverse. It is made up of distinct layers, known as horizons. The five most
common horizons are collectively known as the Master horizons. Figure below depicts a road cut which
shows the multitude of layers that can exist in soil. Though the soil profiles there are two different soils,
that contain distinct surface and subsurface soil layers. Soil profile is important/ useful for farmers,
scientists, ecologists, soil engineers, hydrologists and land use planners.
Road cuts are excellent ways to observe the layers, or horizons, within a soil profile. This particular soil
profile is well developed and consists of many layers.
Components of the Soil Profile
A soil horizon makes up a distinct layer of soil. The horizon runs roughly parallel to the soil surface and
has different properties and characteristics than the adjacent layers above and below. The soil profile
extends from the soil surface to the parent rock material.
The regolith includes all of the weathered material within the profile. The regolith has two components:
the solum and the saprolite.
The solum includes the upper horizons with the most weathered portion of the profile. The saprolite is
the least weathered portion that lies directly above the solid, consolidated bedrock but beneath the
regolith.
Master Horizons
There are 5 master horizons in the soil profile. Not all soil profiles contain all 5 horizons; and so, soil
profiles differ from one location to another. The 5 master horizons are represented by the letters: O, A,
E, B, and C.
O: The O horizon is a surface horizon that is comprised of organic material at various stages of
decomposition. It is most prominent in forested areas where there is the accumulation of debris fallen
from trees.
A: The A horizon is a surface horizon that largely consists of minerals (sand, silt, and clay) and with
appreciable amounts of organic matter. This horizon is predominantly the surface layer of many soils in
grasslands and agricultural lands.
E: The E horizon is a subsurface horizon that has been heavily leached. Leaching is the process in which
soluble nutrients are lost from the soil due to precipitation/erosion or irrigation. The horizon is typically
light in color. It is generally found beneath the O horizon.
B: The B horizon is a subsurface horizon that has accumulated from the layer(s) above. It is a site of
deposition of certain minerals that have leached from the layer(s) above.
C: The C horizon is a subsurface horizon. It is the least weathered horizon. Also known as the saprolite,
it is unconsolidated, loose parent material.
The master horizons may be followed by a subscript to make further distinctions between differences
within one master horizon.
The soil profile develops over time as the result of the weathering of minerals and deposition of organic
matter.
The major Functions of soils are:
Soil organisms are responsible for carrying out many vital functions in the soil. The major Functions of soils
are: •
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Anchor plant roots ,
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Supply water to plant roots,
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Provide air for plant roots ,
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Furnish nutrients for plant growth •
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Release water with low levels of nutrients
Soil microorganisms play key roles in ecosystem functioning. They are known to be influenced by biotic
and abiotic factors, such as plant cover or edaphic parameters.
Topic Two
Biotic and abiotic components of soil
Plants are heavily affected by both the abiotic and biotic properties of the soil in which they are rooted.
Abiotic properties include
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the availability of nutrients and water, which are necessary for plant growth.
These effects of soil properties on the plant can further affect leaf herbivores. These nutrients include
nitrogen and phosphorus
Course work. Discuss different abiotic and biotic components of soil
Topic Three
Soil bacteria
Bacteria are some of the smallest and most abundant microbes in the soil. In a single gram of soil, there
can be billions of bacteria. There are an estimated 60,000 different bacteria species, with particular
roles and capabilities. Most live in the top 10cm of soil where organic matter is present.
Characteristics of Soil bacteria. Some bacteria species are very fragile and can be killed by slight
changes in the soil environment. Other species are extremely tough, able to withstand severe heat, cold
or drying conditions referred to as extremophiles. Some can lie dormant for decades waiting for
favourable conditions. Others can extract nitrogen directly from the air or break down some toxic
substances.
Populations of microbes can boom or bust in the space of a few days in response to changes in soil
moisture, soil temperature or carbon substrate. To gain advantage in this process, many microbes release
antibiotic substances to suppress particular competitors. In this way some species can suppress other
disease-causing microorganisms.
Types of Soil-bacteria
Decomposers
Bacteria play an important role in decomposition of organic materials, especially in the early stages of
decomposition when moisture levels are high. In the later stages of decomposition, fungi tend to
dominate. Bacillus subtilis and Pseudomonas fluorescens are examples of decomposer bacteria.
Nitrogen fixers
Rhizobium bacteria can be inoculated onto legume seeds to fix nitrogen in the soil. These nitrogenfixing bacteria live in special root nodules on legumes such as clover, beans, medic, wattles, alfalfa etc.
They extract nitrogen gas from the air and convert it into forms that plants can use. This form of nitrogen
fixation can add the equivalent of more than 100kg of nitrogen per hectare per year. Azotobacter,
Azospirillum, Agro bacterium, Gluconobacter, Flavobacterium and Herbaspirillum are all examples
of free-living, nitrogen-fixing bacteria, often associated with non-legumes. To date, inoculating the soil
with these organisms has not proved an effective means of increasing nitrogen fixation for non-legume
crops.
Disease suppressors
Bacillus megaterium is an example of a bacterium that has been used on some crops to suppress the
disease-causing fungus Rhizoctonia solani. Pseudomonas fluorescens may also be useful against this
disease. Bacillus subtilis has been used to suppress seedling blight of sunflowers, caused by Alternaria
helianthi. A number of bacteria have been commercial as worldwide for disease suppression.
However, suppression is often specific to particular diseases of particular crops and may only be
effective in certain circumstances.
Aerobes and anaerobes
Aerobic bacteria are those that need oxygen, so where soil is well drained aerobes tend to dominate.
Anaerobes are bacteria that do not need oxygen and may find it toxic. This group includes very ancient
types of bacteria that live inside soil aggregates. Anaerobic bacteria favour wet, poorly drained soils and
can produce toxic compounds that can limit root growth and predispose plants to root diseases.
Actinobacteria
These soil bacteria help to slowly break down humates and humic acids in soils. Actinobacteria
prefer non-acidic soils with pH higher than 5.
Sulfur oxidisers
Many soil minerals contain sulfides but this form of sulfur is largely unavailable to plants. Thiobacillus
bacteria can covert sulfides into sulfates, a form of sulfur which plants can use.
Most people think of bacterial diseases affecting animals and humans but plants can also succumb to
bacterial infections. Bacteria can enter through cuts our other areas of damage that occur in the leaves
or stems due to wind bending the plant, objects hitting the plant, aphids sucking the plant sap or animals
grazing on it. The symptoms then depend on which internal tissues and structures the infection takes a
hold in.
Although thousands of species of bacteria can cause disease in animals and humans, a much smaller
number, probably about one hundred, are able to infect plants and damage them. Bacterial plant diseases
are generally due to bacilli, bacteria that are shaped by rods, some of which are gram negative bacteria
and some of which are gram positive. The majority of plant diseases due to bacterial infection occur
in parts of the world that have a tropical weather pattern.
How Bacteria Damage Plants
When pathogenic bacteria gains entry to a plant it causes one of four main problems that leads to unhealthy plant. Some bacteria produce enzymes that break down the cell walls of plants anywhere in the
plant. They do this to break open to cell to gain access to the nutrients inside but the plant cells affected
die quickly, causing parts of the plant to start rotting. This is why plant diseases that develop due to
cell wall degrading enzymes are generally known as a type of 'rot'.
Some bacteria produce toxins that are damaging to plant tissues generally, usually causing early death
of the plant. Others produce large amounts of polysaccharide sugars that have long chains and are very
sticky. As these travel in the water carrying vessels, the xylem, they block the narrow channels,
preventing water getting from the plant roots up to the shoots and leaves, again causing rapid death of
the plant. Finally, some bacteria produce proteins that mimic plant hormones. These lead to
overgrowth of plant tissue and tumours form. These grow rapidly, taking up valuable nutrients and
energy resources that the plant would otherwise use for its own tissue growth and it becomes weakened
and susceptible to attack by other pathogens such as fungi.
Topic Four
Types of Bacteria That Infect Plants
One of the main types of bacteria that cause plant disease are the Proteobacteria. This large group of
bacterial species include bacteria that cause disease in humans, such as Vibrio cholerae, which causes
cholera, and Helicobacter pylori, which is associated with stomach ulcers. Some species of
Proteobacteria live in soil where they fix nitrogen from the air, forming useful compounds that plants
use in their growth. One species, Xanthomonas campestris, which affects plants from the Brassica and
Arabidopsis groups causing black rot. The disease symptoms progress from discoloured leaves to
extensive wilting of all of the stems and leaves, with all the leaves eventually turning yellow. Parts of
the plant start to die and rot and the plant dies completely shortly afterwards.
Xanthomonas campestris causes its effects on the plant by producing large amounts of polysaccharides
that block the xylem vessels that carry water through the plant. So much is produced that the bacteria is
actually grown in culture to obtain these polysaccharides, better known as xanthan gum, a thickener
used in the food industry.
Some species of Mycoplasma-like species of bacteria also cause serious plant disease. These are
bacteria that do not have cell walls and they are introduced into the phloem tissue of plants by
insects such as aphids that suck plant sap. Phloem vessels in plants are part of the transport system
for sugars, which are generally moved from the leaves, where they are made by photosynthesis, to other
parts of the plant, including the roots. Aphids use needle-like mouth parts to puncture plant stems and
tap directly into this rich supply of liquid sugar. The Mycoplasma bacteria grow inside the aphids and
other sap-sucking insects are then introduced into their plant host by a very effective insect hypodermic.
Plants that produce large amounts of sugar are the worst affected – for example coconut plants and sugar
cane. The overall effect of the infection is to weaken the plant, opening it up to other diseases. The
leaves usually lose their colour and another common symptom is green flowers, or an absence of
flowers.
Plant Bacteria and Humans
Although some of the bacteria that infect plants are from the same large groups as bacterial pathogens
in humans, there is no recorded instance of bacteria being passed from plant to person and causing an
infection. Plant bacterial diseases are highly host-specific.
Management of bacteria
Though largely unaffected by cultivation, bacteria populations are depressed by dry conditions, acidity,
salinity, soil compaction and lack of organic matter. Except in the case of certain seed inoculations,
it is very difficult to build desirable populations of bacteria just by adding them to the soil. If populations
of soil bacteria are low, it is probably because conditions are unfavorable, so any new additions are
likely to suffer the same fate. A more effective approach to bacteria management is:
• address soil health problems such as acidity and compaction
• ensure that there is a good ground cover of grass or mulch.
• build organic matter through practices such as green manure crops, mulching, strategic
grazing and minimum tillage.
Each of these measures has multiple benefits and will also support healthy populations of soil bacteria.
Poor drainage encourages undesirable anaerobic bacteria. Reducing compaction and building soil
organic matter will improve water infiltration without compromising moisture storage and will
discourage anaerobic bacteria.
Key points
• Populations of soil bacteria change rapidly depending on moisture, time of year, type of
crop, mulching, etc.
• Healthy populations of soil bacteria are encouraged by ground cover and organic
matter.
Soil fungi
Soil fungi are microscopic plant-like cells that grow in long threadlike structures or hyphae that make
amass called mycelium. The mycelium absorbs nutrients from the roots it has colonized, surface organic
matter or the soil. It produces special hyphae that create the reproductive spores. Some fungi are single
celled (eg yeast). Fungi have many different structures but they can act in similar ways and thus are not
as plant specific in their needs as some soil bacteria such as Rhizobia.
Fungi groups:
There are three functional groups of fungi.
Decomposers
Decomposers or saprophytic fungi convert dead organic matter into fungal biomass (ie their own
bodies), carbon dioxide and organic acids. They are essential for the decomposition of hard woody
organic matter. By consuming the nutrients in the organic matter they play an important role in
immobilising and retaining nutrients in the soil. The organic acids they produce as by products help
create organic matter that is resistant to degradation. Fungi are capable of degrading cellulose, proteins
and lignin, some of which are highly resistant to breakdown.
Mutualists
These fungi develop mutually beneficial relationships with plants. They colonise plant roots where they
help the plant to obtain nutrients such as phosphorus from the soil. Their mass hides roots from pests
and pathogens, and provides a greater root area through which the plant can obtain nutrients.
Mycorrhizal fungi are perhaps the best known of the mutualists. Mycorrhiza means fungus root, and
mycorrhizal fungi grow inside plant roots. Up to 5m of living hyphae of mycorrhizal fungi can be
extracted from 1g of soil.
The four groups of mycorrhizal fungi are arbuscular, ectomycorrhizal,
ericoid and orchid.
Arbuscular mycorrhiza (VAM) are the most common form of mycorrhiza, especially in agricultural
plant associations. This fungi has arbuscles which are growths formed inside the plant root that have
many small projections going into the cells. About 150 arbuscular mycorrhiza species are known. Most
plants (90%) have some sort of association with these fungi except for groups such as the Cruciferae
family (eg mustard, canola, broccoli), Chenopodiaceae (eg spinach, beets, saltbush) and Proteaceae
(banksia, macadamia).
Pathogens
This group includes the well known fungi such as Verticillium, Phytophthora, Rhizoctonia and
Pythium. These organisms penetrate the plant and decompose the living tissue, creating a weakened,
nutrient deficient plant, or death. The pathogenic fungi is usually the dominant organism in the soil.
Soils with high biodiversity have been shown to suppress soil-borne fungal
Fungi perform important functions within the soil in relation to nutrient cycling, disease suppression
and water dynamics, all of which help plants become healthier and more vigorous.
Decompose woody organic matter.
Along with bacteria, fungi are important decomposers of hard to digest organic matter. They use
nitrogen in the soil to decompose woody carbon rich residues low in nitrogen and convert the nutrients
in the residues to forms that are more accessible for other organisms. Mycorrhizal fungi are well known
for their role in assisting plants in the uptake of phosphorus. Ectomycorrhizal fungi can benefit plants
by promoting root branching and increasing nitrogen phosphorus and water uptake due to their large
surface area and internal cellular mechanisms.
-Fungi Improve plant resilience. The sheer size and mass of fungal hyphae help decrease plant
susceptibility to pests, diseases and drought.
-Improve soil structure: Fungal hyphae bind the soil particles together to create water-stable aggregates
which in turn create pore spaces in the soil that enhance water retention and drainage.
Fungi prefer are hard, carbon-rich woody organic matter. This could be dead rotting trees in a forest,
leaf litter on the surface of orchard soils, or plant roots.
Management of soil fungi
There are several things you can do to encourage fungi in your soil.
-Provide a hospitable environment
-To ensure fungi remain in the earth the soil environment must be kept as hospitable as possible.
This means there must be enough food (organic matter), suitable host plants (if necessary), water and
minimal disturbance of the soil.
-Reduce tillage: Tillage has a disastrous effect on fungi as it physically severs the hyphae and breaks up
the mycelium.
-Reduce fungicide use; Broad-spectrum fungicides are toxic to a range of fungi. Their use will result in
a decline in the numbers of beneficial types of fungi.
Fungal Structures in Soil
There are numerous kinds of fungi. About 20,000 species have been identified worldwide. Species are
identified mostly by the structure of their fruiting bodies, the arrangement and types of spores which they
produce.
Majorities
are very small (microfungi).
Many fungi have fruiting bodies which are stalked e.g.
mushroom. This helps to raise the spores some distance off the ground, so that when they are released, they can
easily catch wind currents and be carried to new places.
Fruiting bodies of fungi will generally produce millions of spores. A single fruiting body like a mushroom, may
produce more than 10,000 million spores.
Mycelium is the vegetative part of a fungus, consisting of a mass of branching, thread-like hyphae. Fungal
colonies composed of mycelium are found in and on top of soil and many other substrates. A typical single spore
germinates into a homokaryotic mycelium, which cannot reproduce sexually; when two compatible homokaryotic
mycelia join and form a dikaryotic mycelium; that mycelium may form fruiting bodies such as mushrooms. A
mycelium may be minute or it may be extensive:
Fungi form mats with their mycelial mats can achieve such massive proportions.
Through the mycelium, a fungus absorbs nutrients from its environment. It does this in a two-stage process. First,
the hyphae secrete enzymes onto or into the food source, which break down biological polymers into smaller
units such as monomers. These monomers are then absorbed into the mycelium by facilitated diffusion and active
transport.
Mycelium is vital in terrestrial and aquatic ecosystems for their role in the decomposition of plant material. They
contribute to the organic fraction of soil, and their growth releases carbon dioxide back into the atmosphere.
Microscopic view of a mycelium.
Mycelium as seen under a log
Rhizosphere is the zone of plat roots. The rhizosphere is the region of soil immediately adjacent to and affected
by plant roots. It is a very dynamic environment where plants, soil, micro-organisms, nutrients and water
meet and interact. The rhizosphere differs from the bulk soil because of the activities of plant roots and their
effect on soil organisms.
Living plant roots and soil microbiota
Mycorrhizae include a broad variety of root-fungi interactions characterized by mode of colonization. Essentially
all plants form mycorrhizal associations, and there is evidence that some mycorrbhizae transport carbon and other
nutrients not just from soil to plant, but also between different plants in a landscape. The main groups include
ectomycorrhizae, arbuscular mycorhizae, ericoid mycorrhizae, orchid mycorrhizae, and monotropoid
mycorrhizae.
Monotropoid mycorrhizae are associated with plants in the monotropaceae, which lack chlorophyll. The root
microbiome is the dynamic community of microorganisms associated with plant roots and productivity in a
variety of ways. Members of the root microbiome benefit from plant sugars or other carbon rich molecules.
Individual members of the root microbiome may behave differently in association with different plant hosts or
may change the nature of their interaction (along the mutualist-parasite continuum) within a single host as
environmental conditions or host health change.
Evidence suggests both biotic (such as host and plant neighbor) and abiotic (such as soil structure and nutrient
availability) factors affect community composition.
Root associated microbes -the fungi, bacteria, and archaea living within or on the surface of roots, as well as in
the rhizosphere.
Root symbionts may improve their host's access to nutrients, produce plant-growth regulators, improve
environmental stress tolerance of their host, induce host defenses and systemic resistance against pests or
pathogens or be pathogenic. Parasites consume carbon from the plant without providing any benefit, or providing
too little benefit relative to what they cost in carbon, thereby compromising host fitness. Symbionts may be
biotrophic (subsisting off of living tissue) or necrotrophic (subsisting off of dead tissue).
Fungi that extend beyond the root surface and engage in nutrient-carbon exchange with the plant host are
commonly considered to be mycorrhizal, but external hyphae can also include other endophytic fungi.
Mycorrhizal fungi can extend a great distance into bulk soil, thereby increasing the root system’s reach and
surface area, enabling mycorrhizal fungi to acquire a large percentage of its host plant’s nutrients. In some
ecosystems, up to 80% of plant nitrogen and 90% of plant phosphorus is acquired by mycorrhizal fungi. In return,
plants may allocate about 20-40% of their carbon to mycorrhizae.
Endophytes
Endophytes are bacteria or fungi that live within plant tissue. They may colonize inter-cellular spaces, the root
cells themselves, or both. While some microbes may be purely mutualistic or parasitic, many may behave one
way or the other depending on the host species with which it is associated, environmental conditions, and host
health.
Topic Five
Hosts responses to microbes
A host’s immune response controls symbiont infection and growth rates. If a host’s immune response is not able
to control a particular microbial species, or if host immunity is compromised, the microbe-plant relationship will
likely reside somewhere nearer the parasitic side of the mutualist-parasite continuum. Similarly, high nutrients
can push some microbes into parasitic behavior, encouraging unchecked growth at a time when symbionts are no
longer needed to aid with nutrient acquisition. A host’s immune response controls symbiont infection and growth
rates.
Fungi have the potential to eradicate such pollutants from their environment; unless the chemicals prove toxic to
the fungus. This biological degradation is a process known as bioremediation.
Mycelial mats have been suggested as having potential as biological filters, removing chemicals and
microorganisms from soil and water. The use of fungal mycelium to accomplish this has been termed
mycofiltration. Knowledge of the relationship between mycorrhizal fungi and plants suggests new ways to
improve crop yields.
When spread on logging roads, mycelium can act as a binder, holding new soil in place and preventing washouts
until woody plants can be established.
Roots are colonized by fungi, bacteria and archaea. Because they are multicellular, fungi can extend hyphae from
nutrient exchange organs within host cells into the surrounding rhizosphere and bulk soil.
Different parts of the root are associated with different microbial communities. For example, fine roots, root tips,
and the main root are all associated with different communities and the rhizosphere, root surface, and root tissue
are all associated with different communities likely due to the unique chemistry and nutrient status of each of
these regions. Different plant species, and even different cultivars, harbor different microbial communities
probably due to host specific immune responses and differences in carbon root exudates.
Abiotic mechanisms also affect root microbial community assembly because individual taxa have different
optima along various environmental gradients, such as nutrient concentrations, pH, moisture, temperature, etc. In
addition to chemical and climatic factors, soil structure and disturbance impact root biotic assembly.
Plant pathology
Diseases in plants are caused by pathogens (infectious organisms) and environmental conditions. Organisms
that cause infectious disease include fungi, oomycetes, bacteria, viruses, viroids, virus-like organisms,
phytoplasmas, protozoa, nematodes and parasitic plants. This study also involves the pathogen identification,
disease etiology, disease cycles, economic impact, plant disease epidemiology, plant disease resistance, how
plant diseases affect humans and animals, pathosystem genetics, and management of plant diseases.
Fungi
Most phytopathogenic fungi belong to the Ascomycetes and the Basidiomycetes.
The fungi reproduce both sexually and asexually through the production of spores and other structures. Spores
may be spread long distances by air or water, or in soil.
Fungal diseases may be controlled through the use of fungicides and other agriculture practices. Biotrophic
fungal pathogens colonize living plant tissue and obtain nutrients from living host cells. Necrotrophic fungal
pathogens infect and kill host tissue and extract nutrients from the dead host cells.
Some fungal-plant pathogens include:
Ascomycetes.
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Fusarium spp. (causal Fusarium wilt disease)
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Thielaviopsis spp. (cause canker rot, black root rot, Thielaviopsis root rot)
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Verticillium spp.
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Magnaporthe grisea (causal of rice blast)
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Sclerotinia sclerotiorum ( cottony rot)
Basidiomycetes
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Ustilago spp. (cause smut)
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Rhizoctonia spp.
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Phakospora pachyrhizi (cause soybean rust)
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Puccinia spp. (cause severe rusts of mostly all cereal grains and cultivated grasses)
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Armillaria spp. (the so-called honey fungus species, which are virulent pathogens of trees and produce
edible mushrooms)
Fungus-like organisms
Oomycetes
The oomycetes are not true fungi but are fungus-like organisms. They include some of the most destructive
plant pathogens including the genus Phytophthora, which includes the causal agents of potato late blight and
sudden oak death. Particular species of oomycetes are responsible for root rot.
Oomycetes have similar infection strategies. Oomycetes are capable of using effector proteins to turn off a
plant's defenses in its infection process.
Significant oomycete plant pathogens
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Pythium spp.
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Phytophthora spp
Phytomyxea
Some slime molds in Phytomyxea cause important diseases, including club root in cabbage and its relatives and
powdery scab in potatoes. These are caused by species of Plasmodiophora and Spongospora, respectively.
Crown gall disease caused by Agrobacterium
Most bacteria that are associated with plants are actually saprotrophic and don’t harm the plant itself. However,
a small number, around 100 known species, are able to cause disease. Bacterial diseases are much more
prevalent in subtropical and tropical regions of the world.
Most plant pathogenic bacteria are rod-shaped (bacilli). In order to be able to colonize the plant they have
specific pathogenicity factors.
Five main types of bacterial pathogenicity factors are known: uses of cell wall–degrading enzymes, toxins,
effector proteins, phytohormones and exopolysaccharides.
Pathogens such as Erwinia species use cell wall–degrading enzymes to cause soft rot. Agrobacterium species
change the level of auxins to cause tumours with phytohormones. Exopolysaccharides are produced by bacteria
and block xylem vessels, often leading to the death-plant.
Bacteria control the production of pathogenicity factors via quorum sensing.
Significant bacterial plant pathogens:
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Burkholderia
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Proteobacteria
Xanthomonas spp.
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Pseudomonas spp.
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Pseudomonas syringae . causes tomato plants to produce less fruit, and it "continues to adapt to the
tomato by minimizing its recognition by the tomato immune system."
Phytoplasmas ('Mycoplasma-like organisms') and spiroplasmas
Phytoplasma and Spiroplasma are a genre of bacteria that lack cell walls and are related to the mycoplasmas,
which are human pathogens. Together they are referred to as the mollicutes. They also tend to have smaller
genomes than most other bacteria. They are normally transmitted by sap-sucking insects, being transferred into
the plants phloem where it reproduces.
ViRUSES
Tobacco mosaic virus
There are viruses, viroids and virus-like organisms which affect plants
There are many types of plant virus, and some are even asymptomatic. Under normal circumstances, plant
viruses cause only a loss of crop yield. Therefore, it is not economically viable to try to control them, the
exception being when they infect perennial species, such as fruit trees.
Most plant viruses have small, single-stranded RNA genomes. However, some plant viruses also have double
stranded RNA or single or double stranded DNA genomes.
Plant viruses are generally transmitted from plant to plant by a vector, but mechanical and seed transmission
also occur. Vector transmission is often by an insect (for example, aphids), but some fungi, nematodes, and
protozoa have been shown to be viral vectors. In many cases, the insect and virus are specific for virus
transmission such as the beet leafhopper that transmits the curly top virus causing disease in several crop
plants.
Nematodes
Root-knot nematode galls
Nematodes are small, multicellular wormlike animals. Many live freely in the soil, but there are some species
that parasitize plant roots. They are a problem in tropical and subtropical regions of the world, where they may
infect crops. Root knot nematodes have quite a large host range, they parasitize plant root systems and thus
directly affect the uptake of water and nutrients needed for normal plant growth and reproduction. Nematodes
are able to cause radical changes in root cells in order to facilitate their lifestyle.
Protozoa and algae
There are a few examples of plant diseases caused by protozoa include Phytomonas, kinetoplastid. They are
transmitted as zoospores that are very durable, and may be able to survive in a resting state in the soil for many
years. They have also been seen to transmit plant viruses.
When the motile zoospores come into contact with a root hair they produce a plasmodium and invade the roots.
Some colourless parasitic algae like Cephaleuros also cause plant diseases.
Management of plant disease
Quarantine
A diseased patch of vegetation or individual plants can be isolated from other, healthy growth. Specimens may
be destroyed or relocated into a greenhouse for treatment or study. Another option is to avoid the introduction
of harmful nonnative organisms by controlling all human traffic and activity. Legislation and enforcement of
law are crucial in order to ensure lasting effectiveness.
Cultural practices
Cultural practices include plot terracing, weather anticipation and response, fallowing, crop-rotation, grafting,
seed care, and dedicated gardening. However they are labor-intensive and inadequate.
Plant resistance
Sophisticated agricultural developments now allow growers to choose from among systematically cross-bred
species to ensure the greatest hardiness in their crops, as suited for a particular region's pathological profile.
Breeding practices have been perfected over centuries to produce/engineer disease-resistant crops but with the
advent of genetic manipulation even finer control of a crop's immunity traits is possible.
Chemical
This is involves pesticide application.
Many natural an synthetic compounds can be employed to combat the above threats. This method works by
directly eliminating disease-causing organisms or curbing their spread; however, it has been shown to have too
broad effect, typically, to be good for the local ecosystem. From an economic standpoint, all but the simplest
natural additives may disqualify a product from "organic" status, potentially reducing the value of the yield.
Biological
Crop rotation may be an effective means to prevent a parasitic population from becoming well-established, as
an organism affecting leaves would be starved when the leafy crop is replaced by a tuberous type, etc. Other
means to undermine parasites without attacking them directly may exist.
Integrated
The use of two or more of these methods in combination offers a higher chance of effectiveness.
PLANT DISEASES
Diseases of the shoot system:
Blights
1. Fire blights – this is a bacteria disease affecting apples, pears, most fruit trees, roses. It blackens shoots and
leaves.
2. Alternaria blight (early blight)- it is a fungal disease affecting ornamental plants, vegetables, fruits, shade
trees worldwide. On tomatoes, pepper and potatoes it s referred to as Early blight causing darkened spots on
leaves and shoots. Spores are carried by air-currents.
Control
Transplant resistant varieties and disease-free seeds. Apply fungi Trichoderma harzianum to
soil before plants.
3. Phytophthora Blight – this is caused by Phytophthora fungi
Control – apply pruning on infected branches and immediately remove infected plant. Tomatoes, pepper is
referred to as Late blight
Bacterial blight – affects legumes causes water soaked spots that easily drop-out.
Control:
Apply rotational cropping.
Cankers
Noticed on woody stems causing cracks and sunken areas.
Cytospora cankers – fungal disease attacking stone fruits, spruces. The cankers are circular and discoloured
areas on the bark.
Necteria canker – A fungus that attackes hardwoods, vines, shrubs. They target twigs and wood parks.
Control: Apply pruning and remove affected plants.
ROTS
They attack mushrooms, they decay roots, stems, flowers by fungi and bacteria.
Fruit rots – apply compost tea, Bacillus subtilis and sulphur sprays before planting. Keep soil well drained.
RUSTS
These majority fungi require 2 hosts .
Asparagus rust, they cause brown small twigs.
Control spacing of plants for air circulation, remove and burn infected plants.
WILTS
Plants wilting is due to lack of water. This is due to fungi and bacteria attacking water-conducting system
causing death.
Stewart,s wilt, Fusarium and Verticilliumwilt. They attack flowers, vegetables ant fruits.
Other fungus include:
-Anthracnose fungus causing dead spot on beans, legumes
- Downy mildews which cause abnormal tissues.
- leaf blisters, they curl leafs
- Molds , causes powdery spots
Nematodes- cause reduced weight, lack of vigor , excessive branching of roots, swellings etc. include root knot
nematodes.
Control: plant resistants, solarise soils.
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Scabs- Fungal hardens roots, leaves, stems likes on apples
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Smuts- fungal attacks grasses, grains, corns
Control: apply fallowing, remove and burn infected plants.
-Viruses- affected plants glow slowly.
Control: use of tissues culture, plant certified crops and control insect that spread diseases.
Topic Six
Soil Nutrient Cycling
The minerals and nutrients in the soil are recycled back into the production of crops. A nutrient cycle (or
ecological recycling) is the movement and exchange of organic and inorganic matter back into the production
of living matter. The basic plant nutrient cycle highlights the central role of soil organic matter. Cycling of
many plant nutrients, especially N, P, S, and B, closely follows parts of the Carbon Cycle. Plant residues and
manure from animals fed forage, grain, and other plant-derived foods are returned to the soil. This organic
matter pool of carbon compounds becomes food for bacteria, fungi, and other decomposers. As organic matter
is broken down to simpler compounds, plant nutrients are released in available forms for root uptake and the
cycle begins again.
All Life on Earth are based on carbon. Water and simple organic compounds such as carbon dioxide become
elaborated into complex, carbon-based organic structures. These compounds include other elements besides
carbon, oxygen and hydrogen. Nitrogen is found in nucleic acids, amino acids and proteins. Phosphorous is a
component of nucleic acids, lipids, energy storage compounds and other organic phosphates.
The phosphorus cycle.
Living things use phosphorus compounds in the synthesis of nucleotides, phospholipids, and phosphorylated
proteins. Phosphorus enters the soil and water as phosphate ions, such as calcium phosphate, during the
breakdown of crops, decaying garbage, leaf litter, and other sources. In the phosphorus cycle, microorganisms
use phosphorus in the form of calcium phosphate, magnesium phosphate, and iron phosphate. They release the
phosphorus from these complexes and assimilate the phosphorus as the phosphate ion (PO4). This ion is
incorporated into DNA, RNA, and other organic compounds using phosphate, including phospholipids. When
the organisms are used as foods by larger organisms, the phosphorus enters and is concentrated in the food
chain.
The sulfur cycle.
Sulfur makes up a small percentage of the dry weight of a cell (approximately 1 percent), but it is an important
element in the formation of certain amino acids such as cystine, methionine, and glutathione. It is also used
in the formation of many enzymes. Many bacteria have an important place in the sulfur cycle in the soil.
Sulfate-reducing bacteria grow in mud and anaerobic water environments, where they reduce sulfur-containing
amino acids to hydrogen sulfide (H2S). Hydrogen sulfide accumulates in the mud of a swamp and gives the
environment an odor of rotten eggs. In the cycle's next step, photosynthetic sulfur bacteria metabolize the
hydrogen sulfide anaerobically. They oxidize the H2S, thereby releasing the sulfur as elemental sulfur (S).
Elemental sulfur accumulates in the soil. Species of colorless sulfur bacteria, including members of the genera
Thiobacillus, Beggiatoa, and Thiothrix, also metabolize the hydrogen sulfide, converting it to sulfate ions,
which are then made available to plants for amino acid formation.
The carbon cycle.
Most of the organic matter present in soil originates in plant material from dead leaves, rotting trees, decaying
roots, and other plant tissues. Animal tissues enter the soil after death. In the carbon cycle, soil bacteria and
fungi recycle the carbon of proteins, fats, and carbohydrates by using the organic plant and animal matter in
their metabolism. Without the recycling of carbon, life would suffer an irreversible decline as nutrients essential
for life which bound in complex molecules. The organic matter of organisms is digested by extracellular
microbial enzymes into soluble products. Fungi and bacteria then metabolize the soluble organic products to
simpler products such as carbon dioxide and acetic, propanoic, and other small acids, as well as other materials
available for plant growth. These elements are made available to the root systems of plants. Undigested plant
and animal matter becomes part of the humus.
The oxygen cycle.
In the oxygen cycle, oxygen is a key element for the chemical reactions of cellular respiration (glycolysis,
Krebs cycle, electron transport, chemiosmosis). The atmosphere is the chief reservoir of oxygen available for
these processes. Oxygen is returned to the atmosphere for use in metabolism by photosynthetic green plants and
photosynthetic microorganisms such as cyanobacteria. During the process of photosynthesis, these organisms
liberate oxygen from water and release it to the atmosphere. The oxygen is then available to heterotrophic
organisms for use in their metabolism.
The Nitrogen Cycle
Renewable resources can be recycled for reuse through the interactions of natural processes of metabolism.
Microorganisms are essential in the webs of metabolic activities that renew the earth's natural resources.
Among the most important biogeochemical cycles is the nitrogen cycle. Nitrogen is a key cellular element of
amino acids, purines, pyrimidines, and certain coenzymes. The element accounts for about 9 to 15 percent of
the dry weight of a cell. Proteins and other organic compounds of life could not be formed without nitrogen.
Ammonification. In the nitrogen cycle, many organisms obtain their nitrogen from organic sources such as
amino acids or purines, while others obtain it from inorganic compounds such as nitrogen gas (N 2), ammonia
(NH 3), or nitrate (NO 3 ‐1). Before nitrate or nitrogen gas can be used, however, the nitrogen in the compounds
must be changed into ammonia, a process called Ammonification. The ammonia is then brought into the living
system by an enzyme‐catalyzed pathway in which glutamic acid and glutamine form. These amino acids are
then used to synthesize other nitrogen compounds in the cell.
Nitrogen fixation. The principal reservoir of nitrogen on earth is the atmosphere, which contains about 80
percent nitrogen. In the process of nitrogen fixation, nitrogen gas from the atmosphere is used to form ammonia
by the chemical process of reduction. Nitrogen fixation is performed by free-living bacteria as well as by
bacteria growing in symbiosis with leguminous plants (plants that bear their seeds in pods, such as peas, beans,
alfalfa, clover, and soybeans). Nitrogen fixation is accomplished by species of Rhizobium inhabiting the roots
of leguminous plants in a mutually beneficial (symbiotic) relationship. These Gram-negative bacteria penetrate
the root hairs and form an infection thread that becomes a root nodule. Here the bacteria fix atmospheric
nitrogen, while deriving nutrients from the plant.
There are many genera of free-living bacteria that exist apart from legumes and fix nitrogen in the soil.
Among the important ones are species of Azotobacter, Azospirillum, Bacillus, Beijerinckia, and
numerous species of cyanobacteria.
Once nitrogen has been incorporated into ammonia, the ammonia is used for various organic substances. Later,
when plants, animals, and microorganisms die, the nitrogen is recycled by forming ammonia once again in the
process of ammonification. For example, proteins and nucleic acids are broken down first to amino acids and
purines and then to acids, gases, and ammonia. Ammonification also occurs from animal excretory products
such as urea, the major component of the urine. The urea is broken down by urea-digesting bacteria, and
ammonia is released.
Nitrification.
The conversion of ammonia to nitrate (NO3-1) is the process of nitrification. Nitrifying
bacteria, such as species of Nitrosomonas and Nitrosococcus, are involved. Nitrosomonas species convert
ammonia to nitrite (NO2-1); then Nitrosococcus species convert the nitrite to nitrate (NO3-1). Nitrification
occurs in soils, fresh water, and marine environments. The nitrate that results serves as an important nitrogen
source for plants.
Denitrification. Denitrification is the process in which the nitrogen of nitrate is released as gaseous nitrogen.
This process makes nitrogen available to bacteria that use it for nitrogen fixation. Denitrification is
accomplished by numerous bacteria that reduce nitrite (NO2-1) to nitrous oxide (N2O) and then to atmospheric
nitrogen (N2).
The prevailing climate and the growing vegetation also influence greatly the nature and abundance of the
microorganisms that inhabit the particular soil. Soil microbes play a crucial role in returning nutrients to their
mineral forms, which plants can take up again. This process is known as mineralization. Biological nitrogen
fixation contributes about 60% of the nitrogen fixed on Earth. Some soil microbes produce a variety of
substances that promote plant growth.