A lecture on the microbial flora inhabiting soil .

1. MICROBIAL
ECOLOGY OF SOIL
PRESENTED BY
ALIZAY
MICROBIAL ECOLOGY
THE WOMEN UNIVERSIT Y MULTAN

2. SOIL AS AN ENVIRONMENT FOR
MICROORGANISMS
• The word soil refers to the loose outer material of Earth’s surface, a layer distinct
from the bedrock that lies underneath
• Soil develops over long periods of time through complex interactions among the
parent geological materials (rock, sand, glacial drift materials, and so on), the
topography, climate, and the presence and activities of living organisms.
• Soil is very dynamic and is formed in a wide variety of environments.
• Formation of organic matter and the growth of plants depend on the microbial
community within the soil

3. T H E S O I L H A B I TAT
A typical soil habitat contains a
mixture of clay, silt, and sand along
with soil organic matter.
Roots, animals (e.g., nematodes
and mites), as well as
chemoorganotrophic bacteria
consume oxygen, which is rapidly
replaced by diffusion within the soil
pores where the microbes live.
Note that two types of fungi are
present: mycorrhizal fungi, which
derive their organic carbon from
their symbiotic partners—plant
roots;
and saprophytic fungi, which

4. SOILS, PLANTS, AND NUTRIENTS
• Soils can be divided into two general categories:
• A mineral soils are derived from the weathering of rock and other inorganic materials.
• Mineral soils contains less than 20% organic carbon.
• An organic soil possesses at least this amount. organic soils are derived from sedimentation in
bogs and marshes.
• Most soils are a mixture of these two basic types. But the vast majority of Earth’s soils are
predominately mineral.
• Vegetated soils have at least four components. These include
1. inorganic mineral matter typically 40% or so of the soil volume
2. organic matter, usually about 5%
3. air and water, roughly 50%
4. microorganisms and macroorganisms, about 5%.

5. SOIL ORGANIC MATTER
• Soil organic matter (SOM) helps to retain nutrients, maintain soil structure, and hold water
for plant use.
• Microbial degradation of plant material results in the evolution of CO2 and the incorporation
of the plant carbon into additional microbial biomass.
• However, a small fraction of the decomposed plant material remains in the soil as SOM.
• Nitrogen & Phosphorus in fertilizers also is another important element of the soil ecosystem.

7. MICROORGANISMS IN THE SOIL
ENVIRONMENT
• Most soil prokaryotes are located on the surfaces of soil particles and require water and
nutrients that must be located in their immediate vicinity.
• In a surface soil the bacterial population can approach 10-9 to 10-10 cells per gram dry weight
of soil as measured microscopically.
• Terrestrial filamentous fungi, in comparison, bridge open areas between soil particles or
aggregates.
• Fungi can be present at up to several hundred meters of hyphae per gram of soil and are
exposed to high levels of oxygen.
• Soil insects and other animals such as nematodes and earthworms contribute to organic
matter transformations in soils.
• These organisms carry out decomposition, often leading to the release of minerals, and
physically “reducing” the size of organic particles such as plant litter.

9. THE PROTEOBACTERIA
• Several α-Proteobacteria show saprophytic lifestyles, but others can interact with
eukaryotic hosts.
• Saprophytic-Rhodobacter spp., Methylomonas
• Well-known examples are the formation of nitrogen-fixing nodules in legumes by
rhizobia and of crown gall diseases by Rhizobium tumefaciens
• The β-Proteobacteria can colonize plant roots efficiently and can be fairly abundant
in various soils.
• Some of these bacteria are known as pathogens of plants and/or animals e.g.,
Erwinia carotovora and Pseudomonas aeruginosa, but they also produce
antibiotics and other bioactive compounds e.g., P. fluorescens, Serratia
plymuthica
• The nitrifying bacteria, belonging to the genera Nitrosomonas and Nitrobacter, fall
into the group of β-Proteobacteria.
• Finally, the sulfate-reducing bacteria make up the greatest part of the δ-
Proteobacteria.

10. Soft rot in potatoe caused by
Erwinia carotovora
Nitrosomonas
Methylomonas
Rhodobacter

11. FIRMICUTES
• Bacillus, Paenibacillus, and Clostridium fall into this group
• The members of these genera are characterized by their capability to
form endospores and survive for long periods of time in soil.
• They can occur in rather high abundance in bulk soil, in the rhizosphere,
on the surface of plant residues, in the gut of invertebrates, or in
association with mycorrhizal fungi
Paenibacillus
colony on plate

12. ACTINOBACTERIA
• Actinobacteria harbor many typical soil bacteria
• They have rather low growth rates and have persistent activities in soil, even under low
nutrient availability.
• Many members of the genus Streptomyces belong to this group.
• They are typical inhabitants of agricultural soils, as well as of the litter layer of forests.
• They produce the sesquiterpene Geosmin, the typical odor compounds of earthy smell
• Belonging to the Actinobacteria are members of the genera Rhodococcus,
Arthrobacter, and Micrococcus
Arthrobacter
Rhodococcus
Streptomyces

13. FUNGI INHABITING SOIL

14. Penicillium
Chytrid
Ustilago
Geosiphon pyrifomis
Rhizopus

15. ALGAE
• Algae have a key ecological role as primary colonizers on bar surfaces (such as volcanic
and desert soils, and rock faces) that are exposed to the sunlight
• This role is further reinforced by the production of carbonic acid as a result of the algal
metabolism
• The release of carbonic acid by algal cell can accelerate the weathering of minerals and
hence, along with the input of organic matter as dead algae cells make a substantial
contribution to soil formation, particularly in its primary stages.
• Algae also produce large amounts of extracellular polysaccharides, which can act as soil
aggregating agents

16. PROTOZOA
• Protozoa are also involved in primary decomposition of soil organic
matter.
• Protozoa take in and process fine organic particles, as well as occurring
in the guts of a number of soil animals, such as termites, where they
play a critical role in the decomposition of cellulosic debris
• Protozoal access to microbial prey may be restricted by pore size
exclusion and by the formation of biofilms on soil particles
• Only cells on the surface of the biofilm will be available to Protozoa.
• Recognition of prey may be restricted if the cells are simply adsorbed to
particles, rather than free in the soil solution
• Their food source is not restricted entirely to microbial prey

17. MICROORGANISM ASSOCIATIONS
WITH VASCULAR PLANTS
• Microbe-plant interactions can be
broadly divided into two classes:
• Microbes that live on the surface of
plants are called epiphytes;
• Those that colonize internal plant
tissues are called endophytes.
• Phyllosphere Microorganisms
• The environment of the aerial portion of a
plant, called the phyllosphere
• It appears that the -proteobacteria
Pseudomonas syringae and Erwinia, and
Pantoea spp. are most important.
• Another abundant bacterial genus,
Sphingomonas, produces pigments that
function like sunscreen so it can survive the
high levels of UV irradiation occurring on
these plant surfaces.

18. RHIZOSPHERE AND RHIZOPLANE MICROORGANISMS
• The plant root surface is termed the
rhizoplane
• Plant roots receive between 30 to 60% of
the net photosynthesized carbon. Of this,
an estimated 40 to 90% enters the soil as
a wide variety of materials including
alcohols, ethylene, sugars, amino and
organic acids, vitamins, nucleotides,
polysaccharides, and enzymes.
• These materials create a unique
environment for soil microorganisms called
the rhizosphere.
• A wide range of microbes in the
rhizosphere can promote plant
growth Plant growth-promoting
rhizobacteria include the genera
Pseudomonas and Achromobacter.
• The process of Nitrogen Fixation is
carried out by representatives of
the genera Azotobacter,
Azospirillum, and Acetobacter.
These bacteria contribute to
nitrogen accumulation by tropical
grasses.

19. MYCORRHIZAE
• Mycorrhizae are mutualistic relationships that develop between most plants and a limited
number of fungal species. Both partners in mutualistic relationships are dependent on the
activities of the other
• Mycorrhizae can be broadly classified as endomycorrhizae—those with fungi that enter the
root cells, or as
• ectomycorrhizae—those that remain extracellular, forming a sheath of interconnecting
filaments (hyphae) around the roots.
• Arbuscular mycorrhizae (AM) are the most common type of mycorrhizae. They can be found
in association with many tropical plants and, importantly, with most crop plants.
• AM are believed to provide a number of services to their plant hosts including protection from
disease, drought, nematodes, and other pests and the ability to provide phosphorous to plant
roots.

21. RHIZOBIA
• Several microbial genera are able to form nitrogen-fixing nodules
with legumes. These include the -proteobacteria
Allorhizobium,Azorhizobium, Bradyrhizobium, Mesorhizobium,
Sinorhizobium, and Rhizobium. Collectively these genera are often
called the rhizobia.
Stem-Nodulating Rhizobia. Nitrogen-fixing
microorganisms also can form nodules on
stems of some tropical
legumes. Nodules formed on the stem of a
tropical legume by a
stem-nodulating Rhizobium.

22. SOILMICROORGANISMS AND HUMAN
HEALTH
• Soils contain a wide variety of pathogenic organisms.
• Organisms such as the protist Acanthamoeba, which can be inhaled from dust,
may cause primary amebic meningoencephalitis.
• Soils are used for surface disposal of human wastes without sewage treatment,
the transmission of a wide variety of pathogens, including protozoa such as
Acanthamoeba and Cyclospora, can occur.
• Soil and soil-related microorganisms also are of concern when they grow in
buildings.
• The major responsible fungi are Stachybotrys chartarum, Eurotium
herbariorum, and Aspergillus versicolor.
• Stachybotrys infection can result in pulmonary hemosiderosis, which causes
bleeding of the lungs and sometimes death.

23. Fungal Growth in a Building.
Fungal growth on sheet rock removed from a
water-damaged building. (a) Stereo microscopic
view showing black discolorations. Bar 500 m.
(b) Scanning electron micrograph of dense
mycelia and conidiophores characteristic of
Stachybotrys.

24. THANK YOU