10.1 Microorganisms in nature ecosystem

10.2 Microbial population interactions

10.3 Biogeochemical cycles

10.4 Plant-microbe interactions

10.5 Bioremediation

Chapter 10 Microbial Ecology

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

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.

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

Protozoa 104 38

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 )

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 )

10.2 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.

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

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

+

+

+

-

-

-

-

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

dead cells and

waste products

Microbialdecomposition 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 organismsNitrification(NH4

+→NO3-)

NH4+→NO2

- Nitrosomonas

NO2-→NO3

- Nitrobacter

Denitrification(NO3-→N2) Bacillus, Pseudomonas

N2 Fixation(N2 +8H → NH3 +H2)

Free-living

Aerobic Azotobacter

Cyanobacteria

Anaerobic Clostridium,purple green bacteria

Symbiotic Rhizobium

Bradyrhizobium. Frankia

Ammonification(organic-N → NH4+)

Many organisms can do this

Sulfur cycle

Key processes and prokaryotes in the sulfur cycle

Processes Organisms

Sulfide/sulfur oxidation(H2S→S0 → SO42-)

Aerobic Sulfur chemolithotrophs

(Thiobacillus, Beggiatoa, many others)

Anaerobic 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 + SO4

2-)

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 oxidationmetal 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 an

d 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 practi

ce 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-enginee

red 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 stud

y?2. populations,guides,communities, ecosystem3. What is the critical characteristic of a mutualistic relationship?4. What is lichen? 5. Schematically describe nitrogen and sulfur cycles and microorgan

isms involved.6. What are prebiotics, probiotics, synbiotics? How do they benefit t

o human or animals?7. Explain how primary secondary and tertiary treatment are accom

plished.8. What is activated sludge ?9. After anaerobic digestion is completed , why is sludge disposal st

ill of concern? How can it be further treated to improve it’s quality?