《微生物學(xué)》課件 Microbiology Chapter 6

1、Chapter 6Microbial Ecology Microbial EcologyMicroorganisms in soil, water, and other environments and how microorganisms act to chemically change their environments.6.1 Microorganisms in soilFew environments on earth have as great a variety of microorganisms as soil. Bacteria, fungi, algae, protozoa

2、 and viruses make up this microscopic menagerie, which may reach a total of billions per gram. The great diversity of the microbial flora makes it extremely difficult to determine accurately the total number of microorganisms present. Cultural methods will reveal only those physiological and nutriti

3、onal types compatible with the cultural environment. Direct microscopic counts theoretically should permit enumeration of all except the viruses, but this technique also has its limitations, especially, in distinguishing living from dead microorganisms. Very often the microbiological analysis of soi

4、l is concerned with the isolation and identification of specific physiological types of microorganisms.For this purpose selective media, differential media, and enriched media are appropriate.6.2. The RhizosphereRhizosphere: The region where the soil and roots make contact is designated the rhizosph

5、ere which is characterized by a zone of increased microbiological activity.Root and Rhizosphere: soil influenced by plant roots The microbial population on and around roots is considerably higher than that of root-free soil. The differences are both quantitative and qualitative. Bacteria predominate

6、, and their growth is enhanced by nutritional substances released from the plant roots, e.g., amino acids, vitamins, and other nutrients. The growth of the plant is influenced by the products of microbial metabolism that are released into soil. It has been reported that amino acid-requiring bacteria

7、 exist in rhizosphere in larger numbers than in the root-free soil. It has been demonstrated that the microorganisms of the rhizoshere is more active physiologically than that of non-rhizosphere soil. The rhizosphere represents a tremendously complex biological system, and there is a great deal yet

8、to be learned about the interactions which occur between the plant and the microorganisms intimately associated with its root system.Electronmicroscope techniques have been developed to observe microorganisms directly on the root surfaces. 6.3 Interactions among soil microorganismsThe microorganisms

9、 that inhabit the soil exhibit many different types of associations or interactions. Some of the associations are neutral; some are beneficial or positive; others are negative or detrimental.6.3.1 Neutral association(1) Neutralism種間共處Two different species of microorganisms inhabit the same environme

10、nt without affecting each other. For example, each could utilize different nutrients without producing metabolic end products that are inhibitory. 6.3.2 positive associations(2) Mutualism共生mutualism is a symbiotic relationship in which each microorganism benefits from the association.Lichen: A mutua

11、listic (or symbiotic) association of an alga and a fungus.mycorrhiza 叢枝吸胞(3) Commensalism(偏利共棲)Commensalism refers to a relationship between microorganisms in which one species of a pair benefits; the other is not affected. For example, many fungi are able to dissimilate cellulose to glucose. Many b

12、acteria are unable to utilize cellulose, but they can use the fungal breakdown products as energy and carbon sources.6.3.3 Negative associations(4) Antagonism拮抗作用The killing, injury, or inhibition of growth of one species of microorganism by another when one organism adversely affects the environmen

13、t of the other. This kind of association is called antagonism.The antagonistic microorganisms may be of great practical importance in biological control, since they often produce antibiotics or other inhibitory substances which affect the normal growth or survival of other microorganisms (pathogenic

14、 microorganisms).(5) CompetitionCompetition is a negative association among species which compete for essential nutrients. In such situation the best adapted microbial species will predominate, or eliminate other species which are dependent upon the same limited nutrient substance.(6) Parasitism寄生Pa

15、rasitism is defined as a relationship between microorganisms in which one lives in or on another. The parasite feeds on the cells, tissues, or fluids of another microorganism, the host, which is commonly harmed in the process. The parasite is dependent upon the host and lives in intimate physical an

16、d metabolic contact with the host. All major groups of plants, animals, and microorganisms are susceptible to attack by microbial parasites.Viruses that attack bacteria, fungi and algae are strict intracellular parasites since they can not be cultivated as free-living forms.Predation捕食Eating of an i

17、ndividual of one species by an individual of another species. Protozoa eat bacteria.6.4 Microorganism and Biogeochemical Cycle Biogeochemical cycle is a process of microbiologically mediated transformation and movement of chemical elements in biosphere. Microorganisms play important roles in biogeoc

18、hemical cycles, because of their metabolic diversity. Lithotrophs use light or inorganic chemical substances as energy source and convert CO2 and H2O into organic compounds. Heterotrophs break down those complex organic molecules and release CO2. 6.4.1 The Carbon CycleCarbon is the most important el

19、ement for all the living organisms. The most rapid means of global transfer of carbon is via the CO2 of the atmosphere. (1) The biogeochemical carbon cycle includes three main processes: Plants and microorganisms (algae, phototrophic bacteria, cyanobacteria, chemolithotops) fix CO2 to synthesize org

20、anic carbon compounds via photosynthesis and chemosynthesis; Carbon dioxide is returned to the atmosphere by respiration of animals, plants and microorganisms; The dead organic material of living organisms is decomposed into CO2 which is released into atmosphere. Microorganisms are the most importan

21、t contributor in the decomposition of dead organic material.The Carbon CycleDecomposition(2) Microbial decomposition of starchStarch is composed of glucose units which are connected by -1, 4-glucosidic bond or -1, 6-glucosidic bond. Many bacteria and fungi are able to produce amylase and phosphoryla

22、se, and hydrolyze starch to glucose. human pancreatic (HPA) a -amylase Aspergillus AmylaseThe fungal species of Aspergillus, Rhizopus and Mucor have strong ability to digest starch. They are widely used in fermentation industries.AspergillumMucorMucor rot on peachRhizopus Rot of Peach RhizopusDecomp

23、osition of starch By amylase By phosphorylaseThe application in practiceProducing the commercial Enzymes;Fermented production, such as alcohol, organic acid, etc.Fermented food: vinegar, liquor, etc.(3) Microbial decomposition of cellulose Cellulose is the most abundant organic matter in the biosphe

24、re. It is estimated that global production of plant material by photosynthesis is 1.51011 tones per year, among which 50 percent is cellulose. Both cellulose and starch are glucose polymers, but the glucose units of cellulose are connected by -1,4-glucosidic bond. Cellulose is much more insoluble th

25、an starch and is less rapidly digested.Many fungi are able to decompose cellulose, For example, Trichoderma, Penicillium, Neurospora and Basidiomycetes. TrichodermaSome bacteria such as Cellulomonas, Cellvibrio, Thermomonospora, Cytophaga, Clostridium and Ruminococcus can also degrade cellulose. Deg

26、radation of Cellulose by Cellulomonas sp. Cellulomonas sp. Thermomonospora curvata - Pellet - culture in liquid medium Two genera of actinomycetes: Streptomyces and Thermomonospora isolated from compost. Cytophaga strain MAR-2 Ruminococcus albus Cellulose-digesting fungi and bacteria are capable of

27、producing cellulases which catalyze the biochemical processes of cellulose decomposition.The cellulases are consisted by the following three enzymes:C1：內(nèi)切酶，使纖維素結(jié)晶分子的H鍵斷裂；Cx復(fù)合酶：C1端斷裂，形成寡聚糖、纖維二糖或葡萄糖；- 葡萄糖糖苷酶：將纖維二、三糖轉(zhuǎn)化成葡萄糖。cellulase of strain Cel48F cellulase of strain Cel9M Decomposition of CelluloseT

28、he application in Practice Producing commercial cellulases Cultivation of mushroom Change the cellulose into humus, increase the soil fertilityAnaerobic Bioreactor Liquids Storage Gas Collection to Generate Energy GroundwaterMonitoring Bioreactor Program Producing the biogas-CH4(4) Microbial degrada

29、tion of xenobioticsXenobiotics are chemically synthesized compounds that are difficult to be degraded by microorganisms. This group of synthetic compounds includes pesticides, polychlorinated biphenyls (PCB), PCP, Plastics, dyes and chlorinated solvents. The accumulation of those products in the env

30、ironment has caused severe pollution, because they are highly recalcitrant.some microorganisms developed new phenotypic characteristics of metabolizing xenobiotics in the process of evolution, due to the close interactions of microorganisms and xenobiotics in the environment. Drug Metabolism Systems

31、 Bacteria can also actively metabolise PAH 4 rings, by dioxygenation followed by ring cleavage. Aliphatic bits can be metabolised by Krebs cycle.Polycyclic aromatic hydrocarbons (PAHs) Many xenobiotics degradable microorganisms can be isolated in nature. The degradation of PCP by Flavobacterium spec

32、ies is the example.6.4.2 The Nitrogen cycleMicrobial involvement in the nitrogen cycle is of great importance, because the major processes of nitrogen transformation are carried out by microorganisms. 6.4.2 The Nitrogen cycleThe nitrogen cycle includes: (1)biological nitrogen fixation; (2) assimilat

33、ion; (3)ammonification; (4) nitrification ; (5) denitrification. Biogeochemical Cycles:NitrogenOrganic Fertilisers and Their Chemical Content Taken from Soil Microbiology; Applications in Agricultural and Environmental Management Edited by F. Blaine Metttting, Jr.6.4.2.1 Biological nitrogen fixation

34、Biological nitrogen fixation is a process of microbial reduction of nitrogen gas to ammonia. NitrogenaseN2+8e+nATP+8H+ 2NH3+H2+nADP+nPiIt has great importance in agriculture and maintaining soil nitrogen fertility. There are diverse groups of microorganisms that can fix nitrogen, and all of them are

35、 prokaryotes. Biological nitrogen fixation can be divided into five classes based on the association of microorganisms and plants, and the niches of biological nitrogen fixation take place. The types of biological nitrogen fixation 類 型代 表 屬固 氮 生 境共生固氮根瘤菌屬，慢生根瘤菌屬固氮根瘤菌屬弗蘭克氏菌屬豆科植物根瘤豆科田菁屬莖瘤非豆科植物根瘤共棲固氮魚腥

36、藻屬蕨類植物小葉內(nèi)內(nèi)生固氮固氮弧菌屬禾本科植物根內(nèi)聯(lián)合固氮固氮螺菌屬植物根表和根圈自生固氮固氮菌屬、類芽胞桿菌屬、梭菌屬植物根圈、堆肥、苗床、沼氣池等Among them, the symbiotic nitrogen fixation of Rhizobium and legumes is well studied and has a great significance in ecology and in agricultural practice.(1) Rhizobia and symbiosis with legumesRhizobia, including genera of Rh

37、izobium, Mesorhizobium, Sinorhizobium, Azorhizobium , BradyrhizobiumAllorhizobium, gram-negative motile rods. The aspects of RhizobiaInfection of the roots of leguminous plants leads to the formation of root nodules. Some stem-nodulating rhizobial strains can infect the stems of the legumes to form

38、stem nodules. Rhizobium nodules on a pea rootNitrogen fixationNNH2H NH2HN NH4H+H3N NH32H+18-24 ATP requiredRoot nodule, for scale see the size of the leaf in the left of the image which is approximately 3 cm longThe picture above shows a clover root noduleHost specificity: however, there is marked h

39、ost specificity between species of legumes and rhizobia.A single rhizobial strain is generally able to infect certain species of legumes and not others. The host specificity is determined by the genotype specific nodulation genes. Effectiveness: The nodules formed are not always able to fix nitrogen

40、. The ability to fix nitrogen is called symbiotic effectiveness. Some strains are effective, others are ineffective. The symbiotic effectiveness is evaluated by the nodule numbers, Plant shoot dry weight yield amount of nitrogen fixed nitrogenase activities in both green-house and field conditions.

41、Usually, there are a large group of rhizobial strains which can infect the plant roots in the rhizosphere, but only the more competitive strains can infect and from nodules. This is called competitiveness. The marker techniques to study rhizobial competitionFAMelanin ProductionAntibiotic resistanceG

42、enes insertion: GusA, Cel B, Lux AB(Reporter gene)AFLPAn effective strain is not always competitive, and vice versa(反之亦然). Soil conditions affect the Rhizobium-legume symbiosis significantly. Compatibility among the rhizobial strains, plant genotypes and soil conditions is very important for high ni

43、trogen-fixing.Root nodule formationThe processes of root nodule formation are illustrated as figure. There are six major steps which include: recognition of the specific partner of both plant and rhizobia and attachment of rhizobia to plant root hairs; excretion of nod factors by rhizobia and causin

44、g root hairs curling; invasion of the root hairs by rhizobia and formation of infection thread;rhizobia in infection thread grow toward root cells, and the invaded plant cells are stimulated to divide; formation of bacteroid state within plant cells;continued plant and rhizobial cell division and fo

45、rmation of the mature root nodules.The root-nodule formation in Rhizobium-legume symbiosis根毛根瘤菌細(xì)胞1.識(shí)別和附著2.根瘤菌分泌Nod因子引起根毛卷曲3.侵染。根瘤菌侵入根毛并且在“侵入線”中增殖4.在侵入線中的根瘤菌向根細(xì)胞生長(zhǎng),被侵染植物細(xì)胞及其附近的細(xì)胞受刺激而分裂侵入線未感染的根毛6.根瘤成熟5.在植物細(xì)胞內(nèi)形成類菌體形式 Nitrogenase and leghemoglobinNitrogenaseThe biochemical process of biological nitrogen

46、 fixation is catalyzed by the enzyme called nitrogenase which is a large two-component protein containing iron and molybdenum. Nitrogenase is sensible to O2. Apparently rhizobia need some O2 to generate energy for growth and for N2 fixation, yet its nitrogenase is inactivated by O2. Root nodule legh

47、emoglobinRoot nodule(Red color) Leghemoglobin However, this contradictory problem can be solved by the O2 binding protein Leghemoglobin in the nodule.Leghemoglobin is red and iron-containing. Its function is to serve as an “oxygen buffer” cycling between the oxidized (Fe3+) and reduced (Fe2+) forms

48、to keep free O2 levels within the nodule at a low but constant level.(2) Other types of biological nitrogen fixationFrankia is a filamentous actinomycete that can infect the roots of some nonleguminous plants to form root nodules and fix nitrogen. These nonlegumes are woody plants and are the pionee

49、r trees able to colonize bare soils at nutrient-poor sites.Some cyanobacteria which have heterocysts, can form symbiosis with a variety of nonleguminous plants, and fix nitrogen. Filamentous Cyanobacterium, Anabaena sp. (SEM x 5,000) Nonfilamentous cyanobacteriaFern Azolla For example, the water fer

50、n Azolla contains a species of heterocystous N2-fixing cyanobacteria called Anabaena azollae within the pores of its fronts. Azolla is important for enriching the soil fertility of rice paddies.AzollaSome bacteria, e.g. Azotobacter, Azospirillum lipoferum, Acetobacter diazotrophicus. are found in th

51、e rhizosphere, or plant root cells, or plant vascular tissues. Acetobacter diazotrophicus These bacteria are free-living, and do not form symbiotic structures with plants. They can fix substantial amounts of N2, which benefits the plant. This group of bacteria is also called “plant growth promoting

52、rhizosphere bacteria” (PGPR).6.4.2.2 AmmonificationProtein is the most important organic nitrogen in nature. Proteolysis is the process of enzymatic hydrolysis by microorganisms capable of elaborating extracellular proteinase, resulting in the release of amino acids. Amino acids are further deaminat

53、ed by ways of hydrolysis, oxidation and reduction. This process is called Ammonification. 6.4.2.3 NitrificationUnder well-drained and neutral pH conditions, nitrifying bacteria convert ammonia to nitrate. This process is called nitrification. The process occurs in two steps. Each step is performed b

54、y different group of nitrifying bacteria. The first step is oxidation of ammonia to nitrite by ammonia-oxidizing bacteria; NO2- + 2H+ + H2O + 276kJO211NH24+ The second step is oxidation of nitrite to nitrate by nitrite-oxidizing bacteria. The nitrifying bacteria are gram-negative chemolithotrophs. T

55、heir main source of carbon is obtained through CO2 fixation. Energy is derived by the oxidation of NH3 or depending upon the group. Although nitrate is readily assimilated by plants, it is very water- soluble and is rapidly leached from soils receiving high rainfall. Consequently nitrification is no

56、t beneficial in environment and agricultural practice.6.4.2.4 DenitrificationThe transformation of nitrate to gaseous nitrogen is accomplished by denitritying bacteria in a series of biochemical reactions. This process is called denitrification which occurs under anaerobic conditions. Denitrifying b

57、acteria are diverse groups of bacteria found in soil, sewage and aquatic environments. They include some chemotrophs, phototrophs, heterotrophs and autotrophs.The environmental conditions in a soil have a significant effect on the level of denitrification. The process is enhanced in soils by (1) oxy

58、gen supply is limited; (2) an abundance of organic matter; (3) elevated temperature( 2565); (4) neutral or alkaline pH.DenitrificationThese are gaseous and escape into the atmosphere.DissimilationAssimilationNH3NON2ON2NH2OHNH3Organic NNO3-NO2-From the point of agriculture, denitrification is an unde

59、sirable process. But from the point of environmental protection, denitrification cad be a very beneficial process in wastewater treatment, where nitrate can be removed from the water, thus minimizing algal growth when the water is discharged into lakes and streams.6.4.3 The sulfur cycleThe sulfur cy

60、cle mainly includes:(1) sulfide and elemental sulfur oxidation; (2) desulfurylation;(3) sulfate reduction. Microorganisms play an important role in this cycle.2S+3O2+2H2O2H2SO4+Q4FeS+O2+2H2SO42Fe2(SO4)3+2H2O+Q(1) Sulfide and elemental sulfur oxidationProtein is one of the most important organic sulf