lecture 15-2 microbial ecology - sjtumicro.sjtu.edu.cn/pdf-microbiology/19-2 lecture 15... ·...

Lecture 15-2 Microbial Ecology

Microbial Habitats, nutrient cycles, and interactions with Plants and Animals

Chen FengSchool of Life Science and BiotechnologyShanghai Jiao Tong Universityhttp://micro.sjtu.edu.cn

Chapter 19 inBROCK BIOLOGY OF MICROORGANISMS

http://micro.sjtu.edu.cn/

Shanghai Jiao Tong University

Chen Chen FengFeng, Shanghai , Shanghai Jiao Jiao Tong UniversityTong University2

15.6. Marine Microbiology

Photic zone-300m where light can reach300-1000m: biological active

• Animals• Chemoorganotrophic microorganims

Below 1000m-deep sea region-relatively biological inactive

III. Marine Microbiology



Archaea/ Bacteria Distribution in ocean

Numbers of prokaryotes in the open oceans decrease with depth. 海洋中原核生物数量随深度减少• In surface waters: cell numbers 105-106 cells/ml• Below 1000m: 103-105 cells/ml.

In general, species of Bacteria predominate in upper waters (<1000m), while numbers are about equal or show a slight predominance of Archaea in lower waters.水深1000m以上时细菌为优势群体, 而深水区古生菌相对数量与细菌持平甚至占优.

Percentage of total prokaryotes belonging to either the Archaea or the Bacteria in North Pacific ocean water



15.7 Deep-Sea Microbiology

Pressure: High • Hydrostatic pressure increases by 1 atm for

every 10m depth• 5000m depth have a pressure of 500 atm

Temperature: Low • Below the 100m depth: 2-3OC

Nutrient levels: Low

Conditions in the deep sea：



High pressure tolerant microorganisms

Barotolerant bacteria耐压细菌• Isolated from depths down to about 3000m• Grow better at 1 atm than 300 atm, do not grow at pressures above 500 atm

Barophilic bacteria嗜压细菌• Isolated from depths between 4000-6000m• Grow optimally at 400atm, can still grow at 1atm

Obligate (extreme) barophilic bacteria极端嗜压菌• Isolated from 10,000m depth• Grow fastest at 700-800atm• Would not grow at pressures of less than 400atm

Barotolerant and barophilic bacteria are also psychrophilic?



IV. THE CARBON AND OXYGEN CYCLES

15.8 The Carbon Cycle15.9 Microbial ecology of intestine in animals:

Syntrophy and Methanogenesis15.10 Carbon Cycling in Ruminant Animals



15.8 The Carbon Cycle

The carbon and oxygen cycles are closely connected, as oxygenic photosynthesis both removes CO2 and produces O2 while respiratory processes both produce CO2 and remove O2.碳循环与氧循环密切相关



15.9 Microbial ecology of intestine in animals动物肠道微生态:

Syntrophy and Methanogenesis互养与甲烷生成



Example: Hindgut of termites 白蚁后肠

A common eastern (USA) subterranean termite worker larva shown beneath a hindgut extracted from a separate worker.



Protozoa and methanogens from the hindgut of the termite

Acetogenesis乙酸生成is the major form of anoxic carbon metabolism in these termites although methanogenesis甲烷生成also occurs.

15.10 Carbon Cycling in Ruminant Animals



Rumen of Ruminant 反刍动物瘤胃

Degradation of cellulose by bacteria and protozoato glucose通过细菌和原生动物来把纤维素分解成葡萄糖Fermentation of glucose to volatile fatty acids(VFAs), CO2 and CH4发酵葡萄糖生成挥发性脂肪酸，CO2及甲烷High concentration of bacteria: source of proteins高浓度的细菌在死亡之后可以为动物提供蛋白质

Rumen and gastro-intestinal system of cow 奶牛的瘤胃与胃肠系统

网胃

重瓣胃

皱胃

瘤胃

食道

Microbial Fermentation in the Rumen

V. OTHER KEY NUTRIENT CYCLES



15.11 The Nitrogen Cycle氮循环

Oxidation reactions are represented by yellowarrows and reductions in red.



15.12 The Sulfur Cycle硫循环

Oxidations are shown in yellow arrows and reductions in red

硫的还原

硫的氧化

硫的歧化反应

脱硫

Thiosulfate



VI. MICROBIAL BIOREMEDIATION生物补救/生物修复

15.13 Microbial leaching of ores15.14 Petroleum biodegradation



15.13 Microbial leaching of ores

If the concentration of metal in the ore is low, it may not be economically feasible to concentrate the mineral by conventional chemical means. Under these conditions, microbial leaching is frequently practiced.如果矿石的金属含量太低，采用化学方法来开采就没有经济价值。这时往往可以采用microbial leaching的方式采矿Especially useful for copper ores because copper sulfate (CuSO4), formed during oxidation of the copper sulfide (CuS) ores, is very water-soluble.

Effect of the bacterium Thiobacillus ferrooxidans on the leaching of copper from the mineral covellite



Leaching process

A typical leaching dump. The low-grade ore has been crushed and dumped in a large pile in such a way. Pipes distribute the acidic leach water over the surface of the pile. The acidic water slowly passes through the pile and exits at the bottom.



(b) Effluent from a copper leaching dump. The acidic water is very rich in dissolved copper.

(c) Recovery of dissolved copper by passage of the copper-rich water over metallic iron in a long flume采用精炼铁制成的长槽



(d) A small pile of recovered copper metal removed from the flume, ready for further purification.

Arrangement of a leaching pile and reactions involved in the microbial leaching of copper sulfide minerals to yield Cu0

(copper metal).此图表示microbial leaching过程中所进行的主要反应步骤



15.14 Petroleum biodegradation

Bioremediation: refers to the cleanup of oil or other pollutants by microorganisms.生物修复/生物补救：指采用微生物的方法来去除油和其它污染物Many bacteria, several molds and yeasts, and certain cyanobacteria and green algae can oxidize hydrocarbons aerobically.许多细菌,一些霉菌和酵母,某些蓝细菌和绿藻可以在有氧时氧化分解碳水化合物.

Hydrocarbon-oxidizing bacteria are able to attach to insoluble oil droplets and can often be seen there in large numbers.烃氧化细菌可以附在不溶性的油滴上生长，并且可以达到很大的数量。

The bacteria are concentrated at the oil-water interface but are not within the droplet itself. 注意它们是在水与油的界面上生长，而不是在油滴的内部。

Hydrocarbon-oxidizing bacteria with oil droplets.



Stimulation of hydrocarbon oxidation by addition of inorganic nutrients通过增加无机营养可促进烃的生物氧化过程

the center rectangular plot was treated with inorganic nutrients to stimulate bioremediation of spilled oil by microorganisms, whereas areas to the left and right were untreated.

Lecture 15-3 Microbial Ecology

Microbial Habitats, nutrient cycles, and interactions with Plants and Animals

Chen FengSchool of Life Science and BiotechnologyShanghai Jiao Tong Universityhttp://micro.sjtu.edu.cn

Chapter 19 inBROCK BIOLOGY OF MICROORGANISMS

http://micro.sjtu.edu.cn/

VII. MICROBIAL INTERACTION WITH PLANTS

微生物与植物的互作



15.15 Lichens and Mycorrhizae地衣与菌根真菌

Lichens地衣• A symbiosis of a fungus and an algae藻类与真菌的

共生体• Grow on rock• Sensitive to air pollution (as a indicator)


Chen Chen FengFeng, Shanghai , Shanghai Jiao Jiao Tong UniversityTong University36 A lichen growing on a branch of a dead tree


Chen Chen FengFeng, Shanghai , Shanghai Jiao Jiao Tong UniversityTong University37Lichens coating the surface of a large rock



Lichen Structure and Ecology

Fungi provide inorganic nutrients to algae and the latter provide organic matter supply to fungi真菌为植物提

供营养而植物为真菌提供有机物



Lichens and Mycorrhizae地衣与菌根真菌

Mycorrhizae (literally means “root fungus”)菌根真菌A symbiosis between plant root and fungus植物根与真菌的共生体Nutrient absorption to plants and organic matter supply to fungi真菌为植物提供营养而植物为真菌提供有机物

Mycorrhizal菌根. In ectomycorrhizae, fungal cells form an extensive sheath around the outside of the root with only little penetration into the root tissue. In endomycorrhizae, the fungal mycelium becomes deeply embedded within the root tissue.外生菌根真菌与内生菌

根真菌

Fig 19.53 Typical ectomycorrhizal root of pine with rhizomorphs of fungus.典型的松树外生菌根,带有真菌的根状菌束



Agrobacterium and crown gall disease-cross talking between bacterium and plantTumor formation in plantsGenetic engineering of plants

15.16 Agrobacterium and crown gall disease农杆菌/土壤杆菌与冠瘿病

Overview of events of crown gall disease following infection of a susceptible plant by Agrobacterium tumefaciens. Note that it is only the T-DNA portion of the Tiplasmid that is transferred to the plant



Recognition and DNA transfer

Attachment to wound sites• Receptor in plant-pectin• Polysaccharide containing β-glucans in bacteria

Signal transduction• vir genes encode proteins that are essential for T-DNA transfer.

vir gene expression is induced by plant signal molecules synthesized by sounded plant tissues.

• Inducers are phenolic compound from plant wound tissue

Figure 19-56 Structure of the Ti plasmid. T-DNA is the region actually transferred to the plant. vir, virulence genes; onc, oncogenes(tumorigenesis genes); ops, opine synthesis genes. Arrows indicate the direction of transcription of each gene.

Signal transduction and DNA transformation

VirA activates VirG by phosphorylation

VirD is an endonuclease

VirE is a single-stranded DNA-binding protein

VirB acts as a conjugation bridge betweenAgrobacterium and the plant cell



15.17 Root Nodule Bacteria and Symbiosis with Legumes

Legume plantsRhizobiumSymbiotic nitrogen fixation

Section 19.22

Formation of root nodule



Organization of the nod gene cluster on the Sym plasmid of Rhizobium leguminosarum biovar viciae, the species that nodulates peas. The product of nodD controls transcription of other nod genes. The nod boxes are highlighted in red, and the arrows indicate the direction oftranscription of nod genes.

Figure: 19-64

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