Chapter 9 Microbial Ecology
Microbial ecology =? Environmental microbiology
The term microbial ecology is now used in a general way
to describe the presence and distributions of
microorganisms.
Microbial ecology is the the study of the behavior and
activities of microorganisms in their natural environments.
Environmental microbiology,in comparison,relates
primarily to all- over microbial processes that occur in a
soil,water or food,as examples,It is not concerned with
the particular microenvironment where the
microorganisms actually are functioning,but with the
broader-scale effects of microbial presence and
activities.
9.1 Microorganisms in nature ecosystem
9.2 Microbial population interactions
9.3 Biogeochemical cycles
9.4 Plant-microbe interactions
9.5 Bioremediation
Chapter 9 Microbial Ecology
9.1 Microorganisms in nature ecosystem
1,Microorganisms and microenvironment
2,Terrestrial Environments
3,Freshwater Environments
4,Marine Environments
9.1.1 Microorganisms and microenvironment
populations
guilds
communities
ecosystem
Metabolically related populations constitute
groupings called guilds.
Sets of guilds conducting complementary
physiological processes interact to form
microbial communities.
In a microbial ecosystem individual cells
grow to form populations.
Community 3
Microbial communities then interact
with communities of macroorganisms
to define the entire ecosystem.
The distribution of microorganisms in nature
ecosystem depends on the resources (nutrients)
available and on the growth conditions,
Temperature,pH,water availability,light,
oxygen of a habitat define the niche for each
particular microorganism.
Soil particles are not homogeneous in terms of their
oxygen content,The outer zones of a small soil particle
may be fully oxic,whereas the center,only a very short
distance away,can remain completely anoxic,
A soil aggregate composed
of mineral and organic
components,showing that
localization of soil microbes,
Very few microorganisms
are found free in the soil
solution; most of them
occur as microcolonies
attached to the soil particles.
9.1.2,Terrestrial Environments
Proportion of different soil microorganisms in soil
Microbial number and biomass in
cultivated field soil（ 15 cm）
Microbes Numbers / g Biomass (g / m3）
Bacteria 108 160
Fungi 105 200
Actinomycetes 105 - 106 160
Algae 104 - 105 32
Protozoa 104 38
Agrobacterium Alcaligenes
Arthrobacter Bacillus
Caulobacter Cellulomonas
Clostridium Corynebacterium
Flavobacterium Micrococcus
Mycobacterium Pseudomonas
Staphylcoccus
Main types of soil microorganisms
The rhizosphere is the soil region
in close contact with plant roots.
Within the rhizosphere,the plant roots
exert a direct influence on the soil bacteria,
This influence is known as the
rhizosphere effect,
In the rhizosphere,microbial populations reach much
higher densities in the rhizosphere than in the free soil.
Rhizosphere Effect
( R/S ratio )
(1) removing hydrogen sulfide,which is toxic to the
plant roots
(2) increasing solubilization of mineral nutrients
needed by the plant for growth
(3) synthesizing vitamins,amino acids,auxins,
gibberellins that stimulate plant growth
(4) antagonizing potential plant pathogens through
competition and the production of antibiotics
Microbial populations in the
rhizosphere may benefit the plant by:
1,neutralism (中性关系 )
2,commensalism (偏利关系 )
3,synergism (协同关系 )
4,mutualism (互惠关系 )
5,competition (竞争关系 )
6,antagonism (拮 抗关系 )
7,parasitism (寄生关系 )
8,predation (捕食关系 )
9.2 Microbial population interactions
Neutralism,there is no any physiological
effect between the populations.
Commensalism is a unidirectional relationship
between populations in which one population
benefits and the other one is unaffected.
Synergism indicates that both populations
benefit from the relationship but the association
is not obligatory,Both populations are capable
of surviving independently.
Mutualism
Symbiosis is an obligatory interrelationship
between two populations that benefits both of
them,
Lichens is composed of a fungus and an alga.
Competition occurs when two populations are
striving for the same resource of nutrients or
the habitat.
Antagonism occurs when one population
produces a substrate inhibitory to another
population.
Parasitism,the parasite population is
benefited and the host population is harmed.
Predation is a widespread phenomenon
where the predator engulfs or attacks the
prey,The prey can be larger or smaller than
the prey,and this normal results in the death
of the prey.
Classification of population interaction
0,No effect; +,positive effect; -,negative effect.
EFFECT OF INTERACTION
NAME OF
INTERACTION
POPULATION
A
POPULATION
B
Neutralism
Commensalism
Synergism
Mutualism
Competition
Amensalism
Parasitism
Predation
0
0
+
+
-
0 or +
+
+
0
+
+
+
-
-
-
-
9.3 Biogeochemical cycles
1,Carbon cycle
2,Nitrogen cycle
3,Sulfur cycle
4,Iron cycle
Carbon cycle
Carbon cycle
Carbon dioxide is incorporated,or fixed,into organic
compounds by such photoautotrophs as cyanobacteria,green
plants,algae,and green and purple sulfur bacteria,
Chemoheterotrophs consume the organic compounds,animals
eat photoautotrophs,especially green plants,and may in turn
be eaten by other animals,
When the organisms die,the organic compounds of their bodies
are deposited in the soil and are decomposed by microorganisms,
principally by bacteria and fungi,During this decomposition,
carbon dioxide is returned to the atmosphere,
Nitrogen cycle
Proteins from
dead cells and
waste products
Microbial
decomposition Amino
acids
Amino
acids
Ammonia
(NH3)
ammonification
Almost all the nitrogen in the soil exists in organic molecules,primarily in
proteins,When an organism dies,the process of microbial decomposition
results in the hydrolytic breakdown of proteins into amino acids.
The amino groups of amino acids are removed and converted into ammonia
(NH3),Ammonification is brought about by numerous bacteria and fungi.
NH4+ N02-Nitrosomonas
Ammonium ion Nitrite ion
N02- N03-
Nitrite ion Nitrate ion
Nitrobacter
Nitrification involves the oxidation of the ammonium ion to nitrate
The genera Nitrosomonas and Nitrobacter are autotrophic
nitrifying bacteria,These organisms obtain energy by oxidizing
ammonia or nitrite,In the first stage,Nitrosomonas oxidizes
ammonium to nitrites,In the second stage,such organisms as
Nitrobacter oxidize nitrites to nitrates
Key processes and prokaryotes in the nitrogen cycle
Processes Example organisms
Nitrification(NH4+→NO 3-)
NH4+→NO 2- Nitrosomonas
NO2-→NO 3- Nitrobacter
Denitrification(NO3-→N 2) Bacillus,Pseudomonas
N2 Fixation(N2+8H → NH 3 +H2)
Free-living
Aerobic Azotobacter
Cyanobacteria
Anaerobic Clostridium,purple green bacteria
Symbiotic Rhizobium
Bradyrhizobium,Frankia
Ammonification(organic-N → NH 4+)
Many organisms can do this
Sulfur cycle
Key processes and prokaryotes in the sulfur cycle
Processes Organisms
Sulfide/sulfur oxidation(H2S→S 0 → SO42-)
Aerobic Sulfur chemolithotrophs
(Thiobacillus,Beggiatoa,many others)
Anaerobic Purple and green phototrophic
bacteria,some chemolithotrophs
Sulfate reduction(anaerobic)(SO42- → H 2S)
Desulfovibrio,Desulfobacter
Sulfur reduction(anaerobic) (S0 → H 2S)
Desulfuromonas,many
hyperthermophilic Archaea
Sulfur disproportionation(S2O32- → H 2S + SO42-)
Desulfovibrio and others
Organic sulfur compound oxidation or reduction(CH3SH→CO 2+ H2S)
(DMSO→DMS)
Desulfurylation(organic-S → H 2S)
Many organisms can do this
9.4 Plant-microbe interactions
1,Lichens and Mycorrhizas
2.The plant environment
3,Root nodule bacteria and symbiosis with
legumes
Lichens
Lichens are leafy or encrusting growths that are widespread in
nature and are often found growing on bare rocks,tree trunks,
house roofs,and surfaces of bare soils, The lichen plant consists
of a symbiosis of two organisms,a fungus and an alga,Lichens
consist of a tight association of many fungal cells within which
the algal cells are embedded,
Mycorrhizas
Mycorrhiza literally means "root fungus" and refers to
the symbiotic association that exists between plant roots
and fungi,Probably the roots of the majority of terrestrial
plants are mycorrhizal,There are two classes of
mycorrhizae,ectomycorrhizae,in which fungal cells
form an extensive sheath around the outside of the root
with only little penetration into the root tissue itself,and
endomycorrhizae,in which the fungal mycelium is
embedded within the root tissue.
Mycorrhizas
? Type of Mycorrhizas,Ectomycorrhiza and
Endomycorrhiza
? Morphology and Function of Mycorrhizal Infection
? Mycorrhiza and Plant Nutrition
? Application Potential of VAM in Agricultural
practice and Ecosystem
? Development and Application of Molecular Probes
? Construction and Analysis of Genomic Library
Mycorrhizas
Ectomycorrhizas
Endomycorrhizas
Ectendomycorrhizas
Functions of mycorrhiza
Root Nodule Bacteria and Symbiosis with Legumes
? Stages in Nodule Formation
? Biochemistry of Nitrogen Fixation in Nodules
? Genetics of Nodule Formation,nod Genes
? Genetic Cooperativity in the Rhizobium-legume
Symbiosis
? Construction and Application of Genetic-
engineered Rhizobium
Symbiosis of Frankia and Non-leguminous Plant
? Morphology and Physiological Characteristic of
Frankia
? Hosts
? Application Potential
8.5 Bioremediation
1,Pollutants
2,Means of bioremediation
Pollutants
1,Microorganisms are an important part of ecosystems
2,Microbial communities are complex
3,Microbial growth requires nutrients and all of which
must be present in usable forms
4,Most microorganisms normally associated with higher
organisms and those grown in the lab,tend to be less able
to compete and survive in soils and waters
5,Extreme environments restrict the range of microbial
types which are able to survive and function
Concepts
Microorganisms in Nature
? Distribution of microorganisms In:
? Soil
? Water
? Air
? Food
? With plants and animals
Proportion of different soil microorganisms in soil
Agrobacterium Alcaligenes
Arthrobacter Bacillus
Caulobacter Cellulomonas
Clostridium Corynebacterium
Flavobacterium Micrococcus
Mycobacterium Pseudomonas
Staphylcoccus
Main types of soil microorganisms
Microbial number and biomass in
cultivated field soil（ 15 cm）
Microbes Numbers / gram Biomass（ g/m3）
Bacteria 108 160
Fungi 105 200
Actinomycetes 105 - 106 160
Algae 104 - 105 32
Protozoa 104 38
The rhizosphere is the soil region
in close contact with plant roots.
Within the rhizosphere,the plant roots
exert a direct influence on the soil bacteria,
This influence is known as the
rhizosphere effect,
In the rhizosphere,microbial populations reach much higher
densities in the rhizosphere than in the free soil,
Rhizosphere Effect
R/S
Microbial populations in the rhizosphere may benefit the plant by:
(1) removing hydrogen sulfide,which is toxic to the plant roots
(2) increasing solubilization of mineral nutrients needed by the
plant for growth
(3) synthesizing vitamins,amino acids,auxins,gibberellins that
stimulate plant growth
(4) antagonizing potential plant pathogens through competition
and the production of antibiotics
Microorganisms in water and air
Microbial ecology =? Environmental microbiology
The term microbial ecology is now used in a general way
to describe the presence and distributions of
microorganisms.
Microbial ecology is the the study of the behavior and
activities of microorganisms in their natural environments.
Environmental microbiology,in comparison,relates
primarily to all- over microbial processes that occur in a
soil,water or food,as examples,It is not concerned with
the particular microenvironment where the
microorganisms actually are functioning,but with the
broader-scale effects of microbial presence and
activities.
9.1 Microorganisms in nature ecosystem
9.2 Microbial population interactions
9.3 Biogeochemical cycles
9.4 Plant-microbe interactions
9.5 Bioremediation
Chapter 9 Microbial Ecology
9.1 Microorganisms in nature ecosystem
1,Microorganisms and microenvironment
2,Terrestrial Environments
3,Freshwater Environments
4,Marine Environments
9.1.1 Microorganisms and microenvironment
populations
guilds
communities
ecosystem
Metabolically related populations constitute
groupings called guilds.
Sets of guilds conducting complementary
physiological processes interact to form
microbial communities.
In a microbial ecosystem individual cells
grow to form populations.
Community 3
Microbial communities then interact
with communities of macroorganisms
to define the entire ecosystem.
The distribution of microorganisms in nature
ecosystem depends on the resources (nutrients)
available and on the growth conditions,
Temperature,pH,water availability,light,
oxygen of a habitat define the niche for each
particular microorganism.
Soil particles are not homogeneous in terms of their
oxygen content,The outer zones of a small soil particle
may be fully oxic,whereas the center,only a very short
distance away,can remain completely anoxic,
A soil aggregate composed
of mineral and organic
components,showing that
localization of soil microbes,
Very few microorganisms
are found free in the soil
solution; most of them
occur as microcolonies
attached to the soil particles.
9.1.2,Terrestrial Environments
Proportion of different soil microorganisms in soil
Microbial number and biomass in
cultivated field soil（ 15 cm）
Microbes Numbers / g Biomass (g / m3）
Bacteria 108 160
Fungi 105 200
Actinomycetes 105 - 106 160
Algae 104 - 105 32
Protozoa 104 38
Agrobacterium Alcaligenes
Arthrobacter Bacillus
Caulobacter Cellulomonas
Clostridium Corynebacterium
Flavobacterium Micrococcus
Mycobacterium Pseudomonas
Staphylcoccus
Main types of soil microorganisms
The rhizosphere is the soil region
in close contact with plant roots.
Within the rhizosphere,the plant roots
exert a direct influence on the soil bacteria,
This influence is known as the
rhizosphere effect,
In the rhizosphere,microbial populations reach much
higher densities in the rhizosphere than in the free soil.
Rhizosphere Effect
( R/S ratio )
(1) removing hydrogen sulfide,which is toxic to the
plant roots
(2) increasing solubilization of mineral nutrients
needed by the plant for growth
(3) synthesizing vitamins,amino acids,auxins,
gibberellins that stimulate plant growth
(4) antagonizing potential plant pathogens through
competition and the production of antibiotics
Microbial populations in the
rhizosphere may benefit the plant by:
1,neutralism (中性关系 )
2,commensalism (偏利关系 )
3,synergism (协同关系 )
4,mutualism (互惠关系 )
5,competition (竞争关系 )
6,antagonism (拮 抗关系 )
7,parasitism (寄生关系 )
8,predation (捕食关系 )
9.2 Microbial population interactions
Neutralism,there is no any physiological
effect between the populations.
Commensalism is a unidirectional relationship
between populations in which one population
benefits and the other one is unaffected.
Synergism indicates that both populations
benefit from the relationship but the association
is not obligatory,Both populations are capable
of surviving independently.
Mutualism
Symbiosis is an obligatory interrelationship
between two populations that benefits both of
them,
Lichens is composed of a fungus and an alga.
Competition occurs when two populations are
striving for the same resource of nutrients or
the habitat.
Antagonism occurs when one population
produces a substrate inhibitory to another
population.
Parasitism,the parasite population is
benefited and the host population is harmed.
Predation is a widespread phenomenon
where the predator engulfs or attacks the
prey,The prey can be larger or smaller than
the prey,and this normal results in the death
of the prey.
Classification of population interaction
0,No effect; +,positive effect; -,negative effect.
EFFECT OF INTERACTION
NAME OF
INTERACTION
POPULATION
A
POPULATION
B
Neutralism
Commensalism
Synergism
Mutualism
Competition
Amensalism
Parasitism
Predation
0
0
+
+
-
0 or +
+
+
0
+
+
+
-
-
-
-
9.3 Biogeochemical cycles
1,Carbon cycle
2,Nitrogen cycle
3,Sulfur cycle
4,Iron cycle
Carbon cycle
Carbon cycle
Carbon dioxide is incorporated,or fixed,into organic
compounds by such photoautotrophs as cyanobacteria,green
plants,algae,and green and purple sulfur bacteria,
Chemoheterotrophs consume the organic compounds,animals
eat photoautotrophs,especially green plants,and may in turn
be eaten by other animals,
When the organisms die,the organic compounds of their bodies
are deposited in the soil and are decomposed by microorganisms,
principally by bacteria and fungi,During this decomposition,
carbon dioxide is returned to the atmosphere,
Nitrogen cycle
Proteins from
dead cells and
waste products
Microbial
decomposition Amino
acids
Amino
acids
Ammonia
(NH3)
ammonification
Almost all the nitrogen in the soil exists in organic molecules,primarily in
proteins,When an organism dies,the process of microbial decomposition
results in the hydrolytic breakdown of proteins into amino acids.
The amino groups of amino acids are removed and converted into ammonia
(NH3),Ammonification is brought about by numerous bacteria and fungi.
NH4+ N02-Nitrosomonas
Ammonium ion Nitrite ion
N02- N03-
Nitrite ion Nitrate ion
Nitrobacter
Nitrification involves the oxidation of the ammonium ion to nitrate
The genera Nitrosomonas and Nitrobacter are autotrophic
nitrifying bacteria,These organisms obtain energy by oxidizing
ammonia or nitrite,In the first stage,Nitrosomonas oxidizes
ammonium to nitrites,In the second stage,such organisms as
Nitrobacter oxidize nitrites to nitrates
Key processes and prokaryotes in the nitrogen cycle
Processes Example organisms
Nitrification(NH4+→NO 3-)
NH4+→NO 2- Nitrosomonas
NO2-→NO 3- Nitrobacter
Denitrification(NO3-→N 2) Bacillus,Pseudomonas
N2 Fixation(N2+8H → NH 3 +H2)
Free-living
Aerobic Azotobacter
Cyanobacteria
Anaerobic Clostridium,purple green bacteria
Symbiotic Rhizobium
Bradyrhizobium,Frankia
Ammonification(organic-N → NH 4+)
Many organisms can do this
Sulfur cycle
Key processes and prokaryotes in the sulfur cycle
Processes Organisms
Sulfide/sulfur oxidation(H2S→S 0 → SO42-)
Aerobic Sulfur chemolithotrophs
(Thiobacillus,Beggiatoa,many others)
Anaerobic Purple and green phototrophic
bacteria,some chemolithotrophs
Sulfate reduction(anaerobic)(SO42- → H 2S)
Desulfovibrio,Desulfobacter
Sulfur reduction(anaerobic) (S0 → H 2S)
Desulfuromonas,many
hyperthermophilic Archaea
Sulfur disproportionation(S2O32- → H 2S + SO42-)
Desulfovibrio and others
Organic sulfur compound oxidation or reduction(CH3SH→CO 2+ H2S)
(DMSO→DMS)
Desulfurylation(organic-S → H 2S)
Many organisms can do this
9.4 Plant-microbe interactions
1,Lichens and Mycorrhizas
2.The plant environment
3,Root nodule bacteria and symbiosis with
legumes
Lichens
Lichens are leafy or encrusting growths that are widespread in
nature and are often found growing on bare rocks,tree trunks,
house roofs,and surfaces of bare soils, The lichen plant consists
of a symbiosis of two organisms,a fungus and an alga,Lichens
consist of a tight association of many fungal cells within which
the algal cells are embedded,
Mycorrhizas
Mycorrhiza literally means "root fungus" and refers to
the symbiotic association that exists between plant roots
and fungi,Probably the roots of the majority of terrestrial
plants are mycorrhizal,There are two classes of
mycorrhizae,ectomycorrhizae,in which fungal cells
form an extensive sheath around the outside of the root
with only little penetration into the root tissue itself,and
endomycorrhizae,in which the fungal mycelium is
embedded within the root tissue.
Mycorrhizas
? Type of Mycorrhizas,Ectomycorrhiza and
Endomycorrhiza
? Morphology and Function of Mycorrhizal Infection
? Mycorrhiza and Plant Nutrition
? Application Potential of VAM in Agricultural
practice and Ecosystem
? Development and Application of Molecular Probes
? Construction and Analysis of Genomic Library
Mycorrhizas
Ectomycorrhizas
Endomycorrhizas
Ectendomycorrhizas
Functions of mycorrhiza
Root Nodule Bacteria and Symbiosis with Legumes
? Stages in Nodule Formation
? Biochemistry of Nitrogen Fixation in Nodules
? Genetics of Nodule Formation,nod Genes
? Genetic Cooperativity in the Rhizobium-legume
Symbiosis
? Construction and Application of Genetic-
engineered Rhizobium
Symbiosis of Frankia and Non-leguminous Plant
? Morphology and Physiological Characteristic of
Frankia
? Hosts
? Application Potential
8.5 Bioremediation
1,Pollutants
2,Means of bioremediation
Pollutants
1,Microorganisms are an important part of ecosystems
2,Microbial communities are complex
3,Microbial growth requires nutrients and all of which
must be present in usable forms
4,Most microorganisms normally associated with higher
organisms and those grown in the lab,tend to be less able
to compete and survive in soils and waters
5,Extreme environments restrict the range of microbial
types which are able to survive and function
Concepts
Microorganisms in Nature
? Distribution of microorganisms In:
? Soil
? Water
? Air
? Food
? With plants and animals
Proportion of different soil microorganisms in soil
Agrobacterium Alcaligenes
Arthrobacter Bacillus
Caulobacter Cellulomonas
Clostridium Corynebacterium
Flavobacterium Micrococcus
Mycobacterium Pseudomonas
Staphylcoccus
Main types of soil microorganisms
Microbial number and biomass in
cultivated field soil（ 15 cm）
Microbes Numbers / gram Biomass（ g/m3）
Bacteria 108 160
Fungi 105 200
Actinomycetes 105 - 106 160
Algae 104 - 105 32
Protozoa 104 38
The rhizosphere is the soil region
in close contact with plant roots.
Within the rhizosphere,the plant roots
exert a direct influence on the soil bacteria,
This influence is known as the
rhizosphere effect,
In the rhizosphere,microbial populations reach much higher
densities in the rhizosphere than in the free soil,
Rhizosphere Effect
R/S
Microbial populations in the rhizosphere may benefit the plant by:
(1) removing hydrogen sulfide,which is toxic to the plant roots
(2) increasing solubilization of mineral nutrients needed by the
plant for growth
(3) synthesizing vitamins,amino acids,auxins,gibberellins that
stimulate plant growth
(4) antagonizing potential plant pathogens through competition
and the production of antibiotics
Microorganisms in water and air
