1、.：.；IntroductionMicrobes are a diverse group of organisms that can be divided into the viruses, unicellular groups (Archaea, Eubacteria, protista, some fungi and some chlorophyta) and a small number of organisms with a simple multicellular structure (the large fungi and chlorophyta).Microbiology: th

2、e science (logos) of small (micro) life (bios). The study of living things so small that they cannot be seen with the naked eye.The three-domain system is a biological classification introduced by Carl Woese that divides cellular life forms into archaea, bacteria, and eukaryote domains. In particula

3、r, it emphasizes the separation of prokaryotes into two groups, originally called Eubacteria (now Bacteria) and Archaebacteria (now Archaea).Microorganisms were first visualized by Antoni van Leeuwenhoek (16321723), a Dutch cloth merchant and an expert lens grinder.The first proof of the involvement

4、 of bacteria in disease and the definitive proof of the germ theory of disease came from the German Robert Koch.Kochs postulates:1, The microorganism must be present in every instance of the disease and absent from healthy individuals.2, The microorganism must be capable of being isolated and grown

5、in pure culture.3 ,When the microorganism is inoculated into a healthy host, the same disease condition must result.4, The same microorganism must be re-isolated from the experimentally infected host.Chapter oneFungi include yeasts, molds, and mushrooms.Viruses are noncellular organisms; they are in

6、tra-cellular parasites of animals, plants, or bacteria. 1, The Prokaryotes can be divided into two kingdoms, Bacteria and Archaea. The classification was first proposed by Woese based on the differences in 16S rRNA sequence.2, Prokaryotic microorganism原核微生物: It is an single-celled organism which doe

7、snt have a nuclear membrane outside the cell nucleus and only has the bare DNA called as the nuclear area.3, Many bacteria are shaped like long rods twisted into spirals or helices; they are called spirilla 螺旋菌if rigid and spirochetes (螺旋體) when flexible.4, Capsules (莢膜) and slime layers (粘液層) usual

8、ly are composed of polysaccharides (多糖), but they may be constructed of other materials.5, Gram staining procedure(革蘭氏染色的步驟)In the first step of the Gram-staining procedure, the smear is stained with the basic dye crystal violet, the primary stain. It is followed by treatment with an iodine solution

9、 functioning as a mordant. That is, the iodine increases the interaction between the cell and the dye so that the cell is stained more strongly. The smear is next decolorized by washing with ethanol or acetone. This step generates the differential aspect of the Gram stain; gram-positive bacteria ret

10、ain the crystal violet, whereas gram-negative bacteria lose their crystal violet and become colorless. Finally, the smear is counterstained with a simple, basic dye different in color from crystal violet. Safranin, the most common counterstain, colors gram-negative bacteria pink to red and leaves gr

11、am-positive bacteria dark purple. 6, The Mechanism of Gram Staining 革蘭氏染色的機(jī)制Although several explanations have been given for the Gramstain reaction results, it seems likely that the difference between gram-positive and gram-negative bacteria is due to the physical nature of their cell walls. If the

12、 cell wall is removed from grampositive bacteria, they become gram negative. The peptidoglycan itself is not stained; instead it seems to act as a permeability barrier preventing loss of crystal violet. During the procedure the bacteria are first stained with crystal violet and next treated with iod

13、ine to promote dye retention. When gram-positive bacteria then are decolorized with ethanol, the alcohol is thought to shrink the pores of the thick peptidoglycan. Thus the dye-iodine complex is retained during the short decolorization step and the bacteria remain purple. In contrast, gram-negative

14、peptidoglycan is very thin, not as highly cross-linked, and has larger pores. Alcohol treatment also may extract enough lipid from the gramnegative wall to increase its porosity further. For these reasons, alcohol more readily removes the purple crystal violet-iodine complex from gram-negative bacte

15、ria. 簡(jiǎn)而言之，不同細(xì)菌的染色差別G+或G-是由于細(xì)胞壁化學(xué)成分的差別而引起了物理特性脫色才干的不同。詳細(xì)而言：經(jīng)過(guò)初染和媒染后，在細(xì)胞膜內(nèi)構(gòu)成了不溶于水的結(jié)晶與碘的復(fù)合物。G+菌由于細(xì)胞壁厚，肽聚糖網(wǎng)層次多而交聯(lián)嚴(yán)密，并且不含類脂，故以乙醇脫色時(shí)不會(huì)溶出縫隙，反而使肽聚糖網(wǎng)孔收縮，使染料滯留在細(xì)胞壁內(nèi)而使其染上紫色；反之，G-菌由于細(xì)胞壁薄，外膜層類脂含量高，肽聚糖層薄和交聯(lián)度差，當(dāng)遇到乙醇時(shí)，以類脂為主的的外膜迅速溶解，這時(shí)薄而松散的肽聚糖網(wǎng)不能阻撓結(jié)晶紫與碘的復(fù)合物的溶出，故細(xì)胞退成無(wú)色。再經(jīng)番紅等紅色染料復(fù)染時(shí)，就使G-菌呈現(xiàn)紅色，而G+菌仍保管紫色或紫紅色。圖示革蘭氏陽(yáng)性菌和革蘭

16、氏陰性菌細(xì)胞壁構(gòu)造。試述革蘭氏陽(yáng)性菌和革蘭氏陰性菌肽聚糖單體的異同點(diǎn)。1四肽尾的第3個(gè)氨基酸不是L-lys，而是被內(nèi)消旋二氨基二酸m-DAP所替代2沒(méi)有特殊的肽橋，其前后兩個(gè)單體間的銜接僅經(jīng)過(guò)甲四肽尾的第4個(gè)氨基酸-D-Ala的羧基與乙四肽尾的第3個(gè)氨基酸-m-DAP的氨基直接相連。Endospore(芽孢)：某些細(xì)菌在其生長(zhǎng)發(fā)育后期，在細(xì)胞內(nèi)構(gòu)成一個(gè)圓形或橢圓形、厚壁、含水量極低、抗逆性極強(qiáng)的休眠體，稱為芽孢。芽孢的構(gòu)造：Endospore-forming process (芽孢的構(gòu)成過(guò)程)鞭毛flagellum的構(gòu)造分為基體、鉤形鞘和螺旋絲; 革蘭氏陰性菌G-基體由L、P、S、M四個(gè)環(huán)構(gòu)成

17、; 革蘭氏陰性菌G+基體由2個(gè)環(huán)構(gòu)成。The systemic taxa of mocroorganisms follow the systemic taxa built by Linnaeus，including seven grades from top to bottom: KingdomPhylum ClassOrderFamilyGenusSpecies All species names of cellular microorganisms obey the Latin binominal nomenclature built by Linnaeus without excepti

18、on.Mycoplasma (支原體)are the procaryotic organism between bacteria (細(xì)菌) and rickettsia (立克次氏體).Chlamydia (衣原體)are a genus of minitype Gram-negative prokaryotic organism which obligate parasitize in eukaryotic cells.Spirochaeta are a group of Gram-negative unicellular prokaryotic organism whose configu

19、ration and kinesiology are particular.Substrate mycelium Aerial hyphae Sporular hyphaMajor Characteristics Used in Taxonomy：1，Classical CharacteristicsMorphological CharacteristicsPhysiological and Metabolic CharacteristicsEcological CharacteristicsGenetic Analysis2, Molecular CharacteristicsCompari

20、son of ProteinsNucleic Acid Base CompositionNucleic Acid HybridizationNucleic Acid Sequencing (16S rRNA sequencing)Bacterial colony (菌落): A bacterial colony is defined as a visible cluster of organisms growing on the surface of or within a solid medium, theoretically cultured from a single cell.Bact

21、erial lawn (菌苔): Bacterial lawn is a used by biologists to describe the appearance of bacterial colonies when all the individual colonies on a petri-dish merge together to form a a field or mat of bacteria.Eukaryotic cellEukaryotic microorganisms真核微生物概念： The eukaryotic microorganisms is not a natura

22、l monophyletic taxon. They have the nuclear membrane coating a cell nucleus, carry out mitosis, and have mitochondria in the cytoplasm. Eukaryotic microorganisms include : fungi, microalgae and protozoa.Fungi differ from plants in two quite fundamental respects: Plants obtain energy from the sun, fu

23、ngi do not;Plants utilize CO2 as a carbon source, fungi do not. One of the features that caused taxonomists finally to remove fungi from the plant kingdom was the distinctive chemical nature of the fungal cell wall. Whereas plant and algal cells have walls composed of cellulose, the cell wall of fun

24、gi is made up principally of chitin.Fungi真菌的概念：This term fungus indicates those organisms that have true nucleus, produce spores by asexual or sexual reproduction, absorb the nourishment material, have no chloroplast. Members of fungi include yeast, mold and mushroom.Major characters of fungi : With

25、 a real nucleus; Having no chloroplast and photosynthesis; Vegetative bodies are usually developing filamentous and branched structure as well as unicell;Typically forming asexual and sexual reproductive spores; Containing chitin in the cell wall; Heterotrophy by absorption; More living adaptively i

26、n the land .Some fungi have long, branched, threadlike filaments called hyphae (菌絲), which aggregate together to form a tangled mycelium (菌絲體). In some fungi the hyphae have crosswalls called septa(橫隔) separating cells, which may nevertheless be joined by one or more pores, which permit cytoplasmic

27、streaming, a form of internal transport.Fungi are categorized into phyla (divisions) based on the type of structures produced during sexual reproduction.(1) Chytridiomycota壺菌亞門(mén)，低等真菌 (2) Zygomycota 接合菌亞門(mén)，低等真菌 (3) Ascomycota 子囊菌亞門(mén)，高等真菌 (4) Basidiomycota 擔(dān)子菌亞門(mén)，高等真菌 (5) Deuteromycota半知菌亞門(mén)，高等真菌真菌的分類Ainsw

28、orth分類系統(tǒng)根據(jù): 橫隔有無(wú)，無(wú)性孢子，有性孢子，典型的代表微生物種類，本人列表。有性孢子的種類和比較見(jiàn)PPT，無(wú)性孢子的種類和比較見(jiàn)PPT，有性繁衍的三個(gè)過(guò)程。rhizoid(假根); Haustorium吸器 Life cycle of fungi:In general, the life cycle involves the fusion of hyphae from two individuals, forming a mycelium that contains haploid nuclei of both individuals. The fusion of hyphae is

29、 called plasmogamy. The fused hyphae containing haploid nuclei from two individuals is heterokaryotic. In some cases, plasmogamy results in cells with one nucleus from each individual. This condition is called dikaryotic. Eventually, two nuclei that originated from different individuals fuse to form

30、 a diploid zygote. Meiosis then produces either four haploid nuclei or four haploid cells. Asexual spores (無(wú)性孢子)are formed by the aerial mycelium of one organism. When these spores germinate, they become organisms that are genetically identical to the parent. Sexual spores (有性孢子) result from the fus

31、ion of nuclei from two opposite mating strains of the same species of fungus. Organisms that grow from sexual spores will have genetic characteristics of both parental strains. VirusVirus病毒的概念：Viruses are a unique group of tiny infectious particles that are obligate parasites of cells, are not cells

32、 but resemble complex molecules composed of DNA or RNA. Most of them are so small (0.02-0.3m) that an electron microscope is necessary to detect them.Structures of viruses: naked virus (nucleic acid, capsid); enveloped virus (nucleic acid, capsid and envelope).Viral capsids have three different form

33、s: helical symmetry, icosahedral symmetry and complex symmetry.噬菌體phage)：侵染細(xì)菌的微生物病毒。 烈性噬菌體virulent phages ：病毒感染宿主細(xì)胞，能在宿主細(xì)胞內(nèi)增殖，產(chǎn)生大量子代噬菌體并引起宿主細(xì)胞裂解的一類噬菌體稱為烈性噬菌體，又稱為毒性噬菌體。病毒可在短時(shí)間內(nèi)能延續(xù)完成吸附、侵入、增殖復(fù)制與生物合成、成熟裝配和裂解釋放5個(gè)階段而實(shí)現(xiàn)其繁衍。含有溫暖噬菌體的寄主細(xì)胞稱為溶源細(xì)胞或細(xì)胞溶源化; 在溶源細(xì)胞內(nèi)的噬菌體核酸稱為原噬菌體或前噬菌體.Replication cycles of virulent pha

34、ge(毒性噬菌體的生活周期): 1, Adsorption (attachment);2, Penetration;3, Replication;4, Assembly;5, Release. one-step growth curve一步生長(zhǎng)曲線：定量描畫(huà)毒性噬菌體生長(zhǎng)規(guī)律的實(shí)驗(yàn)曲線，該曲線反映3個(gè)重要的特性參數(shù)，即埋伏期、裂解期、裂解量.一步生長(zhǎng)曲線可分為三個(gè)時(shí)期：埋伏期是指菌體的核酸侵入宿主細(xì)胞后至第一個(gè)噬菌體粒子裝配前的一段時(shí)間。 Eclipse period：it is the period from the virus penetrating host cell to the re

35、leasing of virion .裂解期是指溶液中噬菌體粒子急劇增多的一段時(shí)間。Burst phase：During this period, the number of virion increases rapidly with lysis of host cell穩(wěn)定期溶液中噬菌體總數(shù)到達(dá)最高點(diǎn)后的時(shí)期。Platform phage：It is the period that all of the host cells are lysated and the valence of virus reaches the apogee.某些噬菌體侵染細(xì)菌后，將本身基因組整合到細(xì)菌細(xì)胞染色體上

36、，隨寄主細(xì)胞分裂而同步復(fù)制，并不引起細(xì)菌裂解釋放噬菌體，因此被稱作溫暖噬菌體temperate phage溫暖性噬菌體和烈性噬菌體生活周期的比較：Prion阮病毒的概念：A prion (= proteinaceous infectious particle) is a self-replicating protein responsible for a range of neurodegenerative disorders in humans and mammals. Inclusion bodies 包涵體的概念：Inclusion bodies are nuclear or cytop

37、lasmic aggregates of stainable substances, usually proteins. They typically represent sites of viral multiplication in a bacterium or a eukaryotic cell and usually consist of viral capsid proteins. Types of insect viruses構(gòu)成包涵體的昆蟲(chóng)病毒類型: NPV核型多角體病毒, CPV 質(zhì)型多角體病毒和GV顆粒型病毒。Growth factors生長(zhǎng)因子：Organic compou

38、nds required because they are essential cell components or precursors of such components and cannot be synthesized by the organism are called growth factors.There are three major classes of growth factors:(1) amino acids, (2) purines嘌呤 and pyrimidines嘧啶, (3) vitamins. Nutritional Types of Microorgan

39、isms：Microorganisms can be classified as either heterotrophs (異養(yǎng)型or autotrophs 自養(yǎng)型with respect to their preferred source of carbon. Phototrophs 光能營(yíng)養(yǎng)型 use light as their energy source; chemotrophs化能營(yíng)養(yǎng)型obtain energy from the oxidation of chemical compounds (either organic or inorganic).The large major

40、ity of microorganisms thus far studied are either photolithotrophic autotrophs 光能自養(yǎng)型or chemoorganotrophic heterotrophs化能異養(yǎng)型A substance can be transported across the cell membrane in one of three ways, known as simple diffusion簡(jiǎn)單分散，facilitated diffusion 協(xié)助分散and active transport自動(dòng)運(yùn)輸?；鶊F(tuán)轉(zhuǎn)位group transloc

41、ation屬于自動(dòng)運(yùn)輸?shù)囊环N特殊方式。比較這四種營(yíng)養(yǎng)物質(zhì)運(yùn)輸方式的異同；Synthetic medium 合成培育基：Such a medium in which all components are known is a defined medium or synthetic medium.Complex media ：Media that contain some ingredients of unknown chemical composition are complex media.Agar瓊脂 is well suited as a solidifying agent because

42、 after it has been melted in boiling water, it can be cooled to about 40 to 42C before hardening and will not melt again until the temperature rises to about 80 to 90C. Agar is also an excellent hardening agent because most microorganisms cannot degrade it.Types of Media：general purpose media；enrich

43、ed (加富media；Selective media；Differential media.Differential media (鑒別培育基)：Differential media are media that distinguish between different groups of bacteria and even permit tentative identification of microorganisms based on their biological characteristics.Enriched (加富media ：Blood and other special

44、 nutrients may be added to general purpose media to encourage the growth of fastidious heterotrophs. These specially fortified media (e.g., blood agar) are called enriched (加富media.Pure culture: a population of cells arising from a single cell.Pure cultures are so important that the development of p

45、ure culture techniques by the German bacteriologist Robert Koch transformed microbiology.The Growth Curve: When microorganisms are cultivated in liquid medium, they usually are grown in a batch culture (分批培育 or closed system. The growth of microorganisms reproducing by binary fission can be plotted

46、as the logarithm of the number of viable cells versus the incubation time, and the resulting curve is called growth curve.The resulting curve has four distinct phases: lag phase, exponential phase, stationary phase and death phase.Measurement of Microbial Growth includes: (1) microbial numbers and (

47、2) microbial masses.Methods for estimating microbial numbers fall into two main categories:(1) those that count total cell numbers;(2) and those that count viable cells only. 延續(xù)培育: 在微生物進(jìn)入對(duì)數(shù)期時(shí)，一方面以一定速度源源不斷地輸入新穎培育液，另一方面漸漸地以同樣速度移去培育物包括菌體和代謝產(chǎn)物，可以延伸對(duì)數(shù)生長(zhǎng)期，這種培育方法稱為延續(xù)培育。Factors affecting microbial growth:Te

48、mperature;pH;Oxygen;Osmotic pressureRadiation;許多化學(xué)物質(zhì)能抑制或殺死微生物，根據(jù)其效應(yīng)可以分為：滅菌sterilization、消毒disinfection和防腐antisepsis.滅菌：利用物理或化學(xué)方法殺死一切微生物及其芽孢、孢子的措施； 消毒：指殺死一切病原微生物； 防腐：是指防止或抑制微生物的生長(zhǎng)繁衍。轉(zhuǎn)化transformation)： 受體菌直接吸收供體菌的DNA片段而獲得后者部分遺傳性狀的景象。 英文概念：Transformation is the uptake by a cell of a naked DNA molecule

49、or fragment from the medium.The transformation frequency of very competent cells is around 10-3 for most genera when an excess of DNA is used.Artificial transformation is carried out in the laboratory by a variety of techniques, including treatment of the cells with calcium chloride(氯化鈣)Transduction

50、轉(zhuǎn)導(dǎo)：Transduction is the transfer of bacterial genes by viruses. Bacterial genes are incorporated into a phage capsid because of errors made during the virus life cycle. The virus containing these genes then injects them into another bacterium, completing the transfer.There are two very different kind

51、s of transduction: generalized transduction (普遍性轉(zhuǎn)導(dǎo)and specialized transduction特異性轉(zhuǎn)導(dǎo)Generalized transduction occurs during the lytic cycle of virulent and temperate phages and can transfer any part of the bacterial genome. During the assembly stage, when the viral chromosomes are packaged into protei

52、n capsids, random fragments of the partially degraded bacterial chromosome also may be packaged by mistake 誤包Transposition 轉(zhuǎn)座：The chromosomes of bacteria, viruses, and eucaryotic cells contain pieces of DNA that move around the genome. Such movement is called transposition.Transposable elements 轉(zhuǎn)座因子

53、：DNA segments that carry the genes required for this process and consequently move about chromosomes are transposable elements.轉(zhuǎn)座子的類型及轉(zhuǎn)座的遺傳效應(yīng)。Microbial ecology微生物生態(tài)學(xué)的概念: Microbial ecology is the study of microbial relationships with other organisms and also with their nonliving environments.Microbia

54、l ecology is the study of the behavior and activities of microorganisms in their natural environments. 二選一 The characteristics of microbial ecosystem微生物生態(tài)系統(tǒng)的特點(diǎn)：1.微環(huán)境microenvironments2.穩(wěn)定性stability3.順應(yīng)性adaptability微生物在生態(tài)系統(tǒng)作用：見(jiàn)PPTBiogeochemical cycling 生物地球化學(xué)循環(huán)：Microorganisms, in the course of their g

55、rowth and metabolism, interact with each other in the cycling of nutrients, including carbon, sulfur, nitrogen, phosphorus, iron, and manganese. This nutrient cycling, called biogeochemical cycling.氮素循環(huán)：四個(gè)概念固氮作用，氨化作用，硝化作用，反硝化作用，五個(gè)環(huán)節(jié)固氮作用，氨化作用，同化作用，硝化作用和反硝化作用，一張圖。見(jiàn)PPT根據(jù)固氮微生物同植物的關(guān)系和固氮的環(huán)境，普通將固氮作用分為3個(gè)類型：

56、自生固氮：微生物單獨(dú)生活時(shí)進(jìn)展固氮。結(jié)合固氮：微生物生活在植物根的外表和黏質(zhì)鞘套內(nèi)，有的進(jìn)入根皮層細(xì)胞之間，但不構(gòu)成特殊構(gòu)造。共生固氮：微生物只需同植物共生時(shí)才干表現(xiàn)固氮活性。Mutualism： Latin mutuus, borrowed or reciprocal 互惠的 defines the relationship in which some reciprocal benefit accrues得利，獲益 to both partners. This is an obligatory relationship in which the mutualist and the host

57、are metabolically dependent on each other. Lichens 地衣are excellent example of mutualism. Lichens are the association between specific ascomycetes (the fungus) and certain genera of either green algae or cyanobacteria.Protocooperation協(xié)同共棲：Protocooperation is a mutually beneficial relationship, simila

58、r to that which occurs in mutualism, but in protocooperation, this relationship is not obligatory.協(xié)同共棲：兩種微生物在群落中雖然單獨(dú)生活，但他們各自的生命活動(dòng)對(duì)其同伴產(chǎn)生有利影響，主要表現(xiàn)為提供營(yíng)養(yǎng)和消除有害要素。Commensalism共生： Latin com, together, and mensa, table is a relationship in which one symbiont, the commensal, benefits while the other (sometim

59、es called the host) is neither harmed nor helped. This is a unidirectional process.微生物之間的對(duì)抗：競(jìng)爭(zhēng)(competition)、拮抗(antagonism)、寄生(parasitism)和捕食predation。競(jìng)爭(zhēng)：爭(zhēng)奪養(yǎng)料或雙方均需求的其他生活條件。拮抗：一種微生物經(jīng)過(guò)產(chǎn)生特殊代謝產(chǎn)物或改動(dòng)環(huán)境條件來(lái)抑制或殺死另一種微生物的景象。拮抗包括：特異性和非特異性拮抗作用。寄生：一種微生物在另一種微生物細(xì)胞中或外表，從后者獲得養(yǎng)料，引起病害或死亡。捕食：一種微生物直接吞食另一種微生物的景象。根瘤菌同豆科植物的共

60、生根瘤；真菌同植物的共生菌根。根圈rhizosphere): 也稱根標(biāo)，指生長(zhǎng)中的植物根系直接影響的土壤區(qū)域，為植物根系有效吸收營(yíng)養(yǎng)的范圍。根圈效應(yīng)rhizosphere effect: 同根圈外土壤中的微生物群落相比，生活在植物根圈中的微生物，在數(shù)量、種類和活性方面都有明顯不同，表現(xiàn)出一定特異性，這種景象稱為根圈效應(yīng)。根土比R/S ratio：根圈中微生物數(shù)量同相應(yīng)的無(wú)根系影響的土壤中微生物數(shù)量之比，是反映根圈效應(yīng)的重要目的。根圈微生物對(duì)植物生長(zhǎng)的影響：一根圈微生物對(duì)植物生長(zhǎng)的有益影響A, 改善植物營(yíng)養(yǎng)；B, 根圈微生物分泌的維生素、氨基酸、生長(zhǎng)刺激素等生長(zhǎng)調(diào)理物質(zhì)能促進(jìn)植物的生長(zhǎng)；C, 根