SOIL MICROBE ECOLOGY

Microorganisms are a fundamentally important

component of the soil habitat where they play
key roles in ecosystem functioning through
controlling nutrient cycling reactions essential
for maintaining soil fertility and also contributing
to the genesis and maintenance of soil structure.
• Within the soil there exist many microbial interactions
with, for example :
• soil invertebrates,
•the rhizosphere (the 3-4 mm layer of soil
surrounding plant roots),
•mycorrhizal fungal associations and plant–
pathogen relationships,
• and these associations contribute to the development
and activity of microbial communities in soils.
The existence of microbes in the soil plays an
important role in biogeochemical cycles and very
responsive to recycling organic compounds.
Soil microbes affect the condition of the
ecosystem in the soil by its contribution in
the :
• provision of plant nutrients
• plant health
• the soil structure
• and soil fertility
Top soil is soil layers richest biological diversity, both
microorganisms (such as bacteria, fungi, yeasts, and
protozoa) and the body of the macro soil (such as
earthworms and arthropods).
All kinds of soil organisms naturally interact with each other
to set the cycle of nutrients through the decomposition of
organic matter (litter and dead organisms) from time to
time on an ongoing basis
Soil microorganisms have the ability to release nutrients
bound in the minerals and turn them into nutrients
available to plants.

Earthworms make the holes and improve water

infiltration and soil aeration to the soil can absorb water
4-10 times higher than on the ground without a
wormhole.

Vertical wormhole can deliver nutrients to the deeper

part to support the development of the root system of
the plant
Biological aspects of soil is very complex and requires a
better understanding, because not much information
about the number and diversity of soil microbes, as well
as how to maintain activity levels in the soil fertility and
productivIty.

This situation is not caused by the substance of the soil

that is alive, dynamic and may change over space and
time. The dynamic nature of the biological status of the
soil provides great opportunities in management.
Biological status of
soil can provide early
warning of
degradation of the
quality of the soil,
making it possible to
implement practices
more sustainable soil
management.
Soil management affect soil biological status has
been widely reported.
• The use of pesticides
• compost or animal manure
• and the introduction of mutants microbes
will affect the structure of microbial
communities in the soil.
• Physical-chemical properties of soil
• the particle size distribution of soil
• presence and age of plant species
• and crop rotation
Are keys factor determinative structure of soil
microbial composition
Microorganisms play an essential role in
# maintaining soil fertility:
# cycling nutrients,
# influencing their availability;
# improving soil structure;
# supporting healthy plant growth;
# degrading organic pollutants.
# Some soil bacteria and fungi cause plant diseases;
# others are antagonistic to plant pathogens and
invertebrate pests.

The rhizosphere provides a region of increased microbial

activity in which certain groups of bacteria and fungi are
more likely to proliferate than in the bulk soil.
Some rhizosphere microorganisms originate from the seed
but the majority are derived from the soil in which a plant
is growing, and they will be returned to the soil, thus bulk
soil and rhizosphere reciprocate impact on microbial
communities.

This is especially important in the case of plant pathogenic

microorganisms and microbial antagonists to pests and
pathogens
Type of plant and soil also affects soil
microbial population dynamics, however,
detailed information about interactions is
not yet available and still need further study.

Soil microbial communities are very difficult

to characterize, for their phenotypic and
genotypic diversity, heterogeneity and
crypticity.
The population of
bacteria in the soil top
soil is> 109 cells / g soil
and the majority can not
be cultured.

Microbial biomass that

can be cultured and
studied further expected
to <5% of the population
Soil microbes have a high degree of heterogeneity.
In a stable system can be hypothesized that the soil
can be occupied by microbes adapted to the soil
environment.

The microbes serve as a biochemical catalyst

processes that take place in the soil, which leads to
changes in the soil.

There are three main factors that contribute to the

dynamics in the soil are the type of crop, soil type
and management techniques
Soil is the growing medium and plants also serve as
microbial growth environment, so that the soil
conditions determine the quality of soil microbes and
plants growing on it.

Good soil microbes or plants have limiting factors in its

growth. Therefore, to achieve the criteria of fertile
land, maintenance of soil biological status is very
important to do
Organic matter content is the most important indicators
and key dynamics of soil fertility.

Organic materials have multifunctional, that is able to

change the physical, chemistry and biological properties of
soil.

Organic materials are also capable of activating compounds

arising from its dynamics as PGR (plant growth regulators),
the source of the enzyme (catalytic reactions in the
metabolism of compounds of life), and biocides (pest and
disease exterminator from organic materials) (Aryantha
1998).
Organic material can alter the biological properties of
the soil by increasing the microbial population in the soil

Increased microbial population (both type and quantity)

dynamics of soil will get better and become healthier
naturally.

Microbes and mycelia, which form the threads serve as

a knitter / adhesive between soil particles, making
better soil structure and increase its resilience in the
face of pressure erodibilitas (destruction) of soil.
The ability to change the biological
properties of the soil towards the
positive can increase the population
of beneficial microbes and plants to
make plants grow healthy crops
without the use of artificial fertilizers
and pesticides
 definition

"Soil borne plant pathogen is a group of microorganisms

that most of its life cycle in the soil, and is able to infect
and cause disease in plants"

Note :
In general, these pathogens have the ability deployment /
dispersal and survive in the soil, and only a few who have
the ability to form spores can be dispersed into the air so
much larger area (Garrett, 1970)
RHIZOSPHERE
Part of soil substrate that
is affected by plant roots
(Hiltner, 1904)
More microbiological
activity compared to those
in the soil away from the
plant roots
Root exudates affect the reproduction and preservation
of pathogens that infect the roots in the soil either
through the soil fungistatic or through inhibition of
number of pathogens in the rhizosphere.

Root exudates may produce essential nutrients for

growth of the antagonist that can suppress the growth of
pathogenic microorganisms in the soil
In general, pathogen has spread from an
infected plant or from the ground.

The pathogen are carried by wind, water (rain,

irrigation water, ground water), insects, and
humans or the tools used (attached to clothing
or shoes, and spread with trim, or the tools of
cultivation)
Patogen dapat menginfeksi tumbuhan ketika:

• Tanaman rentan terhadap penyakit tertentu

• Patogen yang virulen ada (presents)
• Lingkungan (misalnya suhu dan kelembapan)
mendukung berkembangnya penyakit

SEGITIGA PENYAKIT ???

"Knowledge / understanding of the ecology of
pathogens is important to get a method of
managing / controlling"

Example:
Pesticide (fungicide and bactericide) is not
effective if it is applied to control diseases in tea
if the weather is quite wet at a certain period
Disease is an important part of crop protection, but it is
very difficult to recognize / understand in the field
because of its size is very small (difficult for farmers to
recognize the disease, is not as easy to identify pests)

Farmers generally recognize the symptoms caused by

very diverse.

Symptoms of the disease can include stunted plants;

Discoloration; leaves look wilted or dead; the roots are
damaged or die; and other symptoms.
Many fungi that cause disease in plants,
such as tea plants, can survive for long
periods in the soil or on dead vegetation.

They survive well on dead vegetation (as a

source of nutrients), or "dormant" in the
form of spores or other thick-walled
structures. In addition, the fungus can
survive to grow on other living plants near
tea plantation
Most bacteria that cause
disease in plants tea plants
survive in other living near
tea plantations. This can
include a host plants other
than tea plantations, some
weeds, or weeds. In
addition, some bacteria can
survive for long periods in
the soil or on dead
vegetation. Each cell is
dormant bacteria may
protect themselves with a
protective layer that
prevents it from drying (coat
/ capsule)
• Viruses can survive and reproduce only inside
living cells of plants or of some insects.
• Viruses can not survive on dead vegetation or in
the soil.
• The virus can not survive in most insects.
• Only certain sucking insects that carry the virus
that lives in them (especially aphids, white flies
and leaf hoppers).
Nematodes (microscopic worms)
that live in the soil. Most tea
nematodes that cause disease can
not eat or reproduce unless they are
at the roots of living plants.

Some nematodes require tea root,

but others can survive on roots of
some weeds and some wild plants.

Some nematode larvae (immature

stage) could move as far as a few
centimeters through the ground to
look for the roots of new plants.
Some nematodes can be dormant
for months in the ground, "waiting"
roots of plants
Unlike insects, pathogens can not walk or fly into the tea
bushes. Nematodes can move as far as a few
centimeters "seek" the roots of plants. But most
pathogens should be with the "help" (for example, by
wind or rain), or bush tea must "come" to them (eg, root
tea growing against fungal spores). Nonetheless, the
disease can spread rapidly from one plant to another,
and from one area to the next and even one location to
another.
Seeds: pathogens can be performed on or in the
seed plants.

vegetative plant parts: infected transplant can carry

disease from the nursery to the main field. Similarly,
the disease can be transmitted from an infected
mother plants by cuttings.

Growth of pathogens: The fungus can be spread

with the growth of mycelium. For example: the
wood rotting fungi can spread through the soil from
one tree trunk to the next or the active growth.
Wind: The fungi that produce spores on the surface of the
plant can be spread by wind. Example: blister blight, gray
blight, and (presumably) dead end / disease twigs. Some
fungal spores found at an altitude of more than 4000 m
above sea level on top of diseased plants. Often the wind
blows the / spores up to a certain distance, and then the
rain can cause the spores down to the land / other
locations. Some of the bacteria can be spread by wind-
blown rain
Water: Flood or irrigation water can carry pathogens or
spores, especially at or near the ground. Splash water
during heavy rain or dew can spread the fungal spores and
bacteria to different parts of the same plant or nearby
plants.

Soil: the soil there are remnants of plants infected by the

pathogen. Land also include fungal and bacterial spores
and larvae of nematodes. Thus, the disease can be spread
whenever the soil particles are transported, for example,
attached to the roots of seedlings or attached to the
appliance or the shoes
Insects, mites, nematodes can spread
pathogens by chance when spores that
attach to the body of an insect or mite
moves from one plant to another.

More important is the case of some sucking

insects that act as vectors. When the vector
eat the plants sick with the virus, their
mouth or salivary glands become
contaminated with pathogenic virus.
Then, when the vector moves to a healthy plant
and began to eat, pathogens can infect the healthy
plants. Most vectors sucking insects, such as
aphids, white flies and leaf hoppers.

Nematodes can also serve as vectors of

pathogens. Because, nematodes can make small
cuts on the roots can be an entry point for
bacteria and fungi in the soil