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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: the sc
2、ience (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 particular, i
3、t 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 of
4、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 in p
5、ure 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 intra-
6、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 doesn
7、t 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 (螺旋体) when flexible.4, Capsules (荚膜) and slime layers (粘液层) usual
8、ly are composed of polysaccharides (多糖), but they may be constructed of other materials.5, Gram staining procedure(革兰氏染色的步骤)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 （革兰氏染色的机制）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 t
12、he 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 i
13、odine 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-negativ
14、e 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 bac
15、teria. 简而言之，不同细菌的染色差异（G+或G-）是由于细胞壁化学成分的差异而引起了物理特性（脱色能力）的不同。具体而言：通过初染和媒染后，在细胞膜内形成了不溶于水的结晶与碘的复合物。G+菌由于细胞壁厚，肽聚糖网层次多而交联紧密，并且不含类脂，故以乙醇脱色时不会溶出缝隙，反而使肽聚糖网孔收缩，使染料滞留在细胞壁内而使其染上紫色；反之，G-菌由于细胞壁薄，外膜层类脂含量高，肽聚糖层薄和交联度差，当遇到乙醇时，以类脂为主的的外膜迅速溶解，这时薄而松散的肽聚糖网不能阻挡结晶紫与碘的复合物的溶出，故细胞退成无色。再经番红等红色染料复染时，就使G-菌呈现红色，而G+菌仍保留紫色或紫红色。图示革兰氏
16、阳性菌和革兰氏阴性菌细胞壁结构。试述革兰氏阳性菌和革兰氏阴性菌肽聚糖单体的异同点。（1）四肽尾的第3个氨基酸不是L-lys，而是被内消旋二氨基二酸（m-DAP）所代替（2）没有特殊的肽桥，其前后两个单体间的连接仅通过甲四肽尾的第4个氨基酸-D-Ala的羧基与乙四肽尾的第3个氨基酸-m-DAP的氨基直接相连。Endospore(芽孢)：某些细菌在其生长发育后期，在细胞内形成一个圆形或椭圆形、厚壁、含水量极低、抗逆性极强的休眠体，称为芽孢。芽孢的结构：Endospore-forming process (芽孢的形成过程)鞭毛（flagellum）的结构分为基体、钩形鞘和螺旋丝; 革兰氏阴性菌（G-
17、）基体由L、P、S、M四个环构成; 革兰氏阴性菌（G+）基体由2个环构成。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 Linnae
18、us without exception.Mycoplasma (支原体)are the procaryotic organism between bacteria (细菌) and rickettsia (立克次氏体).Chlamydia (衣原体)are a genus of minitype Gram-negative prokaryotic organism which obligate parasitize in eukaryotic cells.Spirochaeta are a group of Gram-negative unicellular prokaryotic orga
19、nism whose configuration and kinesiology are particular.Substrate mycelium Aerial hyphae Sporular hyphaMajor Characteristics Used in Taxonomy： 1，Classical Characteristics Morphological Characteristics Physiological and Metabolic Characteristics Ecological Characteristics Genetic Analysis 2, Molecula
20、r Characteristics Comparison of Proteins Nucleic Acid Base Composition Nucleic Acid Hybridization Nucleic 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 cult
21、ured from a single cell.Bacterial 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
22、microorganisms is not a natural 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
23、obtain energy from the sun, fungi 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
24、cellulose, the cell wall of fungi 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
25、.Major characters of fungi : With 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 abs
26、orption; More living adaptively in the land .Some fungi have long, branched, threadlike filaments called hyphae (菌丝), which aggregate together to form a tangled mycelium (菌丝体). In some fungi the hyphae have crosswalls called septa(横隔) separating cells, which may nevertheless be joined by one or more
27、 pores, which permit cytoplasmic streaming, a form of internal transport.Fungi are categorized into phyla (divisions) based on the type of structures produced during sexual reproduction. (1) Chytridiomycota（壶菌亚门，低等真菌） (2) Zygomycota （接合菌亚门，低等真菌） (3) Ascomycota （子囊菌亚门，高等真菌） (4) Basidiomycota （担子菌亚门，高
28、等真菌） (5) Deuteromycota（半知菌亚门，高等真菌）真菌的分类（Ainsworth分类系统）依据: 横隔有无，无性孢子，有性孢子，典型的代表微生物种类，自己列表。有性孢子的种类和比较（见PPT），无性孢子的种类和比较（见PPT），有性繁殖的三个过程。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
29、 nuclei of both individuals. The fusion of hyphae is 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 tha
30、t originated from different individuals fuse to form a diploid zygote. Meiosis then produces either four haploid nuclei or four haploid cells. Asexual spores (无性孢子)are formed by the aerial mycelium of one organism. When these spores germinate, they become organisms that are genetically identical to
31、the parent. Sexual spores (有性孢子) result from the fusion 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 particl
32、es that are obligate parasites of cells, are not cells 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
33、 and envelope).Viral capsids have three different forms: helical symmetry, icosahedral symmetry and complex symmetry.噬菌体（phage)：侵染细菌的微生物病毒。 烈性噬菌体（virulent phages ）：病毒感染宿主细胞，能在宿主细胞内增殖，产生大量子代噬菌体并引起宿主细胞裂解的一类噬菌体称为烈性噬菌体，又称为毒性噬菌体。病毒可在短时间内能连续完成吸附、侵入、增殖（复制与生物合成）、成熟（装配）和裂解（释放）5个阶段而实现其繁殖。含有温和噬菌体的寄主细胞称为溶源细胞或细胞
34、溶源化; 在溶源细胞内的噬菌体核酸称为原噬菌体（或前噬菌体）.Replication cycles of virulent phage(毒性噬菌体的生活周期): 1, Adsorption (attachment);2, Penetration;3, Replication;4, Assembly;5, Release. one-step growth curve（一步生长曲线）：定量描述毒性噬菌体生长规律的实验曲线，该曲线反映3个重要的特性参数，即潜伏期、裂解期、裂解量.一步生长曲线可分为三个时期：潜伏期是指菌体的核酸侵入宿主细胞后至第一个噬菌体粒子装配前的一段时间。 Eclipse per
35、iod：it is the period from the virus penetrating host cell to the releasing of virion .裂解期是指溶液中噬菌体粒子急剧增多的一段时间。Burst phase：During this period, the number of virion increases rapidly with lysis of host cell稳定期溶液中噬菌体总数达到最高点后的时期。Platform phage：It is the period that all of the host cells are lysated and t
36、he valence of virus reaches the apogee.某些噬菌体侵染细菌后，将自身基因组整合到细菌细胞染色体上，随寄主细胞分裂而同步复制，并不引起细菌裂解释放噬菌体，因而被称作温和噬菌体（temperate phage）温和性噬菌体和烈性噬菌体生活周期的比较：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
37、 mammals. Inclusion bodies （包涵体的概念）：Inclusion bodies are nuclear or cytoplasmic 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（形成包涵体
38、的昆虫病毒类型）: NPV（核型多角体病毒）, CPV （质型多角体病毒）和GV（颗粒型病毒）。Growth factors（生长因子）：Organic compounds 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 a
39、cids, (2) purines（嘌呤） and pyrimidines（嘧啶）, (3) vitamins. Nutritional Types of Microorganisms：Microorganisms can be classified as either heterotrophs (异养型）or autotrophs （自养型）with respect to their preferred source of carbon. Phototrophs （光能营养型） use light as their energy source; chemotrophs（化能营养型）obtai
40、n energy from the oxidation of chemical compounds (either organic or inorganic).The large majority of microorganisms thus far studied are either photolithotrophic autotrophs （光能自养型）or chemoorganotrophic heterotrophs（化能异养型）A substance can be transported across the cell membrane in one of three ways,
41、known as simple diffusion（简单扩散），facilitated diffusion （协助扩散）and active transport（主动运输）。基团转位（group translocation）属于主动运输的一种特殊形式。比较这四种营养物质运输方式的异同；Synthetic medium （合成培养基）：Such a medium in which all components are known is a defined medium or synthetic medium.Complex media ：Media that contain some ingre
42、dients of unknown chemical composition are complex media.Agar（琼脂） is well suited as a solidifying agent because 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 exce
43、llent hardening agent because most microorganisms cannot degrade it.Types of Media：general purpose media；enriched (加富）media；Selective media；Differential media.Differential media (鉴别培养基)：Differential media are media that distinguish between different groups of bacteria and even permit tentative ident
44、ification of microorganisms based on their biological characteristics.Enriched (加富）media ：Blood and other special 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
45、culture: a population of cells arising from a single cell.Pure cultures are so important that the development of pure 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
46、a batch culture (分批培养） or closed system. The growth of microorganisms reproducing by binary fission can be plotted 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, expone
47、ntial phase, stationary phase and death phase.Measurement of Microbial Growth includes: (1) microbial numbers and (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. 连续培养: 在微生物
48、进入对数期时，一方面以一定速度源源不断地输入新鲜培养液，另一方面缓缓地以同样速度移去培养物（包括菌体和代谢产物），可以延长对数生长期，这种培养方法称为连续培养。Factors affecting microbial growth: Temperature; pH; Oxygen; Osmotic pressure Radiation;许多化学物质能抑制或杀死微生物，根据其效应可以分为：灭菌（sterilization）、消毒（disinfection）和防腐（antisepsis）.灭菌：利用物理或化学方法杀死所有微生物及其芽孢、孢子的措施； 消毒：指杀死所有病原微生物； 防腐：是指防止或抑制微生物的生长繁殖。转化（transformation)： 受体菌直接吸收供体菌的DNA片段而获得后者部分遗传性状的现象。 英文概念：Transformation is the uptake by a cell of a naked DNA molecule or fragment from the medium.The transformation freque
