Chapter 10
Microbial Ecology
10.1 Microorganisms in nature ecosystem
10.2 Microbial population interactions
10.3 Biogeochemical cycles
10.4 Plant-microbe interactions
10.5 Bioremediation
10.1 Microorganisms in nature ecosystem
1. Microorganisms and microenvironment
2. Terrestrial Environments
3. Freshwater Environments
4. Marine Environments
10.1.1 Microorganisms and microenvironment
In a microbial ecosystem individual cells grow to
form populations.
Metabolically related populations constitute
groupings called guilds.
Sets of guilds conducting complementary
physiological processes interact to form microbial
communities.
Microbial communities then interact with
communities of macroorganisms to define the
entire ecosystem.
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
104
38
Protozoa
Main types of soil microorganisms
Agrobacterium(脓杆菌)
Alcaligenes(产碱杆菌属)
Arthrobacter(节杆菌)
Bacillus
Caulobacter(柄杆菌)
Cellulomonas(纤维单胞菌属)
Clostridium(梭菌属)
Corynebacterium(棒杆菌属)
Flavobacterium(产黄菌属)
Micrococcus(微球菌属)
Mycobacterium(分枝杆菌属) Pseudomonas(假单胞菌属)
Staphylcoccus(葡萄球菌属)
Rhizosphere Effect
( R/S ratio )
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.
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
10.2 Microbial population interactions
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 )
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.
For example:
Protozoan-termite relationship
Lichens: fungus and green algae
Rumen ecosystem
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
EFFECT OF INTERACTION
NAME OF
INTERACTION
Neutralism
Commensalism
Synergism
Mutualism
Competition
Amensalism
Parasitism
Predation
POPULATION
A
POPULATION
B
0
0
+
+
0 or +
+
+
0
+
+
+
-
0, No effect; +, positive effect; -, negative effect.
10.3 Biogeochemical cycles
1. Carbon cycle
2. Nitrogen cycle
3. Sulfur cycle
4. Iron 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
Microbial
decomposition
dead cells and
waste products
Amino
acids
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.
Amino
acids
ammonification
Ammonia
(NH3)
The amino groups of amino acids are removed and converted into ammonia
(NH3). Ammonification is brought about by numerous bacteria and fungi.
Nitrification involves the oxidation of the ammonium ion to nitrate
NH4
+
Nitrosomonas
Ammonium ion
N02Nitrite ion
N02-
Nitrite ion
Nitrobacter
N03Nitrate ion
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+→NO3-)
NH4+→NO2NO2-→NO3-
Nitrosomonas
Nitrobacter
Denitrification(NO3-→N2)
N2 Fixation(N2 +8H → NH3 +H2)
Free-living
Aerobic
Anaerobic
Symbiotic
Bacillus, Pseudomonas
Azotobacter
Cyanobacteria
Clostridium,purple green bacteria
Rhizobium
Bradyrhizobium. Frankia
Ammonification(organic-N → NH4+)
Many organisms can do this
Sulfur cycle
Key processes and prokaryotes in the sulfur cycle
Processes
Sulfide/sulfur oxidation(H2S→S0 → SO42-)
Aerobic
Anaerobic
Organisms
Sulfur chemolithotrophs
(Thiobacillus, Beggiatoa, many others)
Purple and green phototrophic
bacteria, some chemolithotrophs
Sulfate reduction(anaerobic)(SO42- → H2S)
Desulfovibrio, Desulfobacter
Sulfur reduction(anaerobic) (S0 → H2S)
Desulfuromonas, many
hyperthermophilic Archaea
Sulfur disproportionation(S2O32- → H2S + SO42-)
Desulfovibrio and others
Organic sulfur compound oxidation or reduction(CH3SH→CO2+ H2S)
(DMSO→DMS)
Desulfurylation(organic-S → H2S)
Many organisms can do this
Iron cycles
• Bacterial iron reduction and oxidation
Fe2+ + 1/4O2 + 2OH-1 + 1/2H2O
Fe(OH)3
Ferrous iron oxidation at
acid pH:
Thiobacillus ferrooxidans,
an iron-oxidizing
bacterium, is strict
acidophile, a small number
of cells can be responsible
for precipitating a large
amount of iron.
Pyrite 黄铁矿oxidation
metal bioleaching生物浸矿
• One of the most common forms of iron and sulfur
in nature is pyrite (FeS2), in mining operation, a
slow chemical reaction occurs:
FeS2 + 31/2O2 + H2O
Fe2+ + 2SO42- + 2H+
Fe2+ Thiobacillus ferrooxidans Fe3+
FeS2 + 14Fe3+ + 8H2O
15Fe2+ + 2SO42- + 16H+
Spontaneous
Role of iron-oxidizing bacteria in the oxidation of the mineral pyrite
Probiotics for humans and
animals
• Probiotics:益生菌 living microorganisms or
substances to promote health and growth,
has the potential to reestablish the natural
balance and return the host to normal health
and nutrition.
• Prebiotics: 益生素oligosaccharide寡糖
• Synbiotic: the combination of prebiotics
and probiotic microorganisms.
How Probiotic microorganisms
displace pathogen
• 1. Competition with pathogens for nutrients
and adhesion sites
• 2. Inactivationof pathogenic bacterial toxins
or metabolites
• 3. Production of substance that inhibit
pathogen growth
• 4. Stimulation of nonspecific immunity
Protential health benefits of probiotic
microorganisms for humans
• 1. Anticarcinogenic 抗致癌activity
• 2. Control of intestinal pathogens
• 3. Improvement of lactose use in individuals
who have lactose intolerance
• 4. Reduction in the serum cholesterol
concentration
10.4 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 Geneticengineered Rhizobium
Symbiosis of Frankia and Non-leguminous Plant
•
•
•
Morphology and Physiological Characteristic of
Frankia
Hosts
Application Potential
10.5 Bioremediation
1. Pollutants
2. Means of bioremediation
Wastewater treatment
Waste resource:
industrial、agricultural and human
Materials: organic matter
Measuring water quality
TOC:total organic carbon
COD:chemical oxygen demand
BOD:biochemical oxygen demand(20 ℃ 5days）
Treatment goal
•Removal of dissolved organic matter and
possibly inorganic nutrients
•Inactivation and removal of pathogens
Water Treatment processes
•Primary:can remove 20-30% of the BOD
•Secondary: 90-95%of the BOD and many
bacterial pathogens are removed
•Tertiary：remove nonbiodegradable organic
material、heavy metals、and minerals
Activated sludge treatment
Activated sludge: a recycle system of sludge
of active biomass formed with oxidized and
degraded organic matter
活性污泥结构
丝状微生物：丝状细菌，真菌，藻类。附着生长，具有
大的比表面积
菌胶团：细菌及其分泌的胶质物组成的细小颗粒，是活
性污泥主体，具很强的吸附、氧化分解有机物的能力
关系：相互依存，丝状微生物形成絮体骨架，菌胶团附
着使絮体具有一定沉降性而不易被带走
活性污泥处理污水
Questions
1. What is Microbial Ecology and What do microbial ecologists
study?
2. populations,guides,communities, ecosystem
3. What is the critical characteristic of a mutualistic relationship?
4. What is lichen?
5. Schematically describe nitrogen and sulfur cycles and
microorganisms involved.
6. What are prebiotics, probiotics, synbiotics? How do they benefit
to human or animals?
7. Explain how primary secondary and tertiary treatment are
accomplished.
8. What is activated sludge ?
9. After anaerobic digestion is completed , why is sludge disposal
still of concern? How can it be further treated to improve it’s
quality?