Microbiology （微生物学） Meng Qingheng Bio-DPT. College of Life Science and Chemistry Tjnu. Arrangement • Textbook ： Microbiology –Textbook for bilingual course, Meng Q.H. Sun J.H. • Bibliography： 1.《微生物学》，沈 萍， 主编高等教育出版社 2.《微生物学教程》，周德庆，高等教育出版社， 3. 《微生物学》，武大复旦合编，高等教育出版社 4. Microbiology 6th Ed. 1996. Totora. et. 5. Microbiology 5th Ed. 2002. L. M. Prescott et al www.mhhe.com / prescott 5 • Lecture ：54 h Contents ： I: Morphology and Anatomy II: Physiological Functions III : Diversity & Ecological activities MICROBIOLOGY ( 微生物学 ) Introduction What is Microbiology ? Micro-biology is a branch of Biology that deals with Microbes, and considers the occurrence in nature of the microscopic forms of life, of course their reproduction, physiology, participation in the processes of nature, ecological relationships with other living things and their significances in science and industry. The term Microbes (Microorganism , Germ) is not a classifying (taxonomic) word, it is just used to describe on a kind or a group of organisms that are too small to be seen by our naked eyes without the use of a microscope, such as viruses, bacteria, fungi, protozoa and some algae. In the subject, bacteria are the major objects to be taught and discussed involving their biological features. Viruses and fungi are described only in words of syllabus. The groups include: 细菌 Bacteria Actinomycetse 放线 菌 Mycoplasma 支原体 Chlamydia 衣原体 Rickettsia 立克次氏体 Procaryotes (Monera) （原核生物）（原核界） Cyanobacteria 蓝细菌 Yeast 酵母菌 (Fungi) Mold( mould) 霉 菌 Protozoa Algae Viruses 原生动物 藻类 病毒 （真菌界） Eucaryotes (Protistae) （真核生物） （原生界） ----------- Non-cellular (Vira) （非细胞生物） （病毒界） From the microbes above, you will find that they are belonging to four kingdoms. This is according to the 6 kingdoms system set up by a Chinese scholar 王大耜 in 1979. The 6 kingdoms are : Monera; protistae; fungi; plantae; animalia; vira This system was set up based on the 5 kingdoms system raised by H.R.Whittaker (professor of Cornell Univ.) adopting the concepts of cellular organization and nutritional patterns in 1969. (1969, Science ) The 5 kingdoms are: Monera; Protistae ; Fungi; Plantae; Animalia Why they are grouped into microbial category? — — The characteristics of microorganism 1． Microscopic 2． Independent units 3． Simple in structure 4． Rapid growth rates & variable 5． Omnipresent Microbial world Organisms Infectious agents (dependent-living) (living) Prokaryotes (unicellular) Eubacteria Archaea eukaryotes Algae (unicellular or multicellular viruses Fungi (unicellular or multicellular viroids prions Other Protozoa (unicellular) multicellular organisms Microbes – the Double-Edged Sword We tend to associate these small organisms only with uncomfortable infections, major diseases such as AIDS, SARS, or such common inconveniences as spoiled food. For instance, in 1347, the bubonic plague that swept through Europe led 25 million people (about one third of the European population) to death. Another example is the Irish Famine historically during the mid of 18th century, 1 million people died for the shortage of potato—the food they live on in Ireland, because of the potato blight disease caused by Phytophthora infestans and about 1.2 million people had to emigrated to the other countries. AIDS was first identified in 1981. Since then more than 65 million people have been infected all over the world and almost 25 million of them died. By the end of 2006, over 40 million people live with HIV. It has become a big challenge to human beings in the 21st century. However, the majority of microorganisms make crucial contributions to the world ’ s inhabitants by helping to maintain the balance of living organisms and chemicals in our environment. Marine and freshwater microorganisms form the basis of the food chain in oceans, lakes, and rivers. Soil microbes help break down wastes and incorporate nitrogen gas from the air into organic compounds , thereby recycling chemical elements in the soil, water, and air. Certain bacteria and algae play important roles in photosynthesis, a food-and oxygen-generating process that is critical to life on earth. Humans and many other animals depend on the bacteria in their intestines for digestion and the synthesis of some vitamins that their bodies require, including some B vitamins for metabolism and vitamin K for blood clotting. Microbes have been used for thousands of years, in many processes, to produce food, from brewing and wine making, cheese production and bread making (baking), to the manufacture of soy sauce. As you known, Chinese ancient was one of the original discovers of microbial utilization. A Brief History of Microbiology Experience period Experiment period Microbiology in the Twentieth Century I. Early development of microbiology (Experience period ) ⒈我国古代对微生物的认识 制曲、酿酒方面：距今8000~4500龙山文化时期， 龙山文化遗址出土的陶器中有酒具。公元前14世纪 《书经》记有：若作酒醴，尔惟曲蘖。公元前二世纪 《淮南子》中就有“清醠之美，始于耒耜”之说；晋 代江统所写的《酒诰》（公元三世纪）中曾这样叙述： “酒之所兴，肇自上皇，或云仪狄，一曰杜康。有饭 不尽，委余空桑，郁积成味，久蓄气芳。本出于此， 不由奇方。”。 食用菌种植方面：郭沫若在《中国史稿》一书中 认为，距今6000~7000年前的仰韶文化时期，我们的祖 先已经大量采食蘑菇了。 数千年来，我国历代人民对大型真菌的形态和习性进行了仔细 的观察，创造了丰富的词汇，并做过许多正确的描述：菌，生 木上；蕈，地菌也。除菌、蕈二字外，还有芝、栭、栮等。栮 （栭）生木上，形如耳，故以耳名。芝，神草也，有青、赤、 黄、白、黑、紫六色，芝生于土，土气和，故芝草生。我国古 代在栽培方面也有较为详细的记载。 早在唐代，韩鄂所著的《四时篡要》中的“种菌子”一段就曾 记载：“取烂构木及叶，于地埋之。常以泔浇令湿，雨三日即 生。”又法：“畦中下烂粪，取构木可长六七尺，截断磓碎。 如种菜法，于畦中匀布，土盖。水浇常令润。如初有小菌子， 仰杷推之，明旦又出，亦推之。三度后，出者甚大，即收食之。 本自构木，食之不损人。构又名楮”。从栽培方法上看，应该 是指金针菇，因为在现代栽培方法中有“搔菌”程序，与“仰 杷推之”有异曲同工之处。 在医学方面：《左转》中记载有鲁宣公12年（公元前597 年）叔展所说：“有麦曲呼？曰：无……。河鱼腹疾奈何？” 的一段话。可见公元前六世纪就已知到用微生物治疗腹病。 公元三世纪，已有“取（疯狗）脑傅之”的记载，预防狂犬 病。根据《医宗金鉴》记载：“种痘之法起于江右，达于京 畿。究其起源，为宋真宗时峨眉山有神人出，为丞相王达之 子种痘而愈，其法随传于世。” 可见种痘的方法在宋真宗 时代（998~1022年）已得到应用。到18世纪，英国乡村医生 秦纳（Jenner) 才发明种牛痘的方法。1904年，牛痘法传入我 国，牛痘法简单易行，安全可靠，彻底取代了人痘法。 在农业方面：据考证，远在商代，已知施用经过一定时间 储存的粪便来肥田。春秋时，沤制粪肥的应用更为普遍。后 魏贾思勰所著《齐民要术》（六世纪）指出：种过豆类植物 的土地特别肥沃，提倡轮作。实际上是应用根瘤菌的作用。 而西方采用轮作制则是18世纪30年代以后的事了。公元二世 纪，《神农本草》已有“白僵”的记载。 II. Milestones of Microbiology (Experiment period) The discovery of microorganisms The spontaneous generation conflict The recognition of microbial role in disease The discovery of microbial conversing on organic and inorganic matter The development of microbiology in this century The discovery of microorganisms The first person to accurately observe and describe microorganisms Antony van Leeuwenhock (1632-1723) Antony van leeuwenhoek of Delft, Holland— the first person who observed and described microorganisms was an amateur microscopist. Leeuwenkoek made his simple, single-lens microscope which could amplify the object being viewed 50 – 300 times. Between 1673 – 1723, he wrote a series of letters to the Royal Society of London describing the microbes he observed from the samples of rainwater, and humam mouth. lens Object being viewed adjusting screws A drawing of one of the microscopes showing the lens a; mounting pin b; and focusing screws c and d. Leeuwenhoek’s drawings of bacteria from the human mouth. Conflict over “Spontaneous Generation” As a matter of facts, until late of the nineteenth century, people, particularly scientists and philosophers believed that some of the living organisms could arise from nonliving matter spontaneously. They even believed that toads, snakes, as well as mice could develop from moist soil besides those flies from manure, and the maggots from decaying meat. A representative person was the English priest John Needham (1713-1781). He reported his experiment on spontaneous generation in 1748. Needham found that the heated nutrient broth contained in the covered flasks eventually teemed with microbes and claimed it as vital force. Twenty years later, an Italian priest, also a scientist Lazzaro Spallanzani (1729-1799) showed that flasks sealed before boiled had no growth of microorganisms, and he proposed that air carried germs probably entered the Needham’s culture medium. He also commented that external air might be required to support the growth of microbes already in the medium. In answer to the criticism, Needham claimed that the vital force had been destroyed by the heat and kept out by the seals. The debate over spontaneous generation continued until 1861, when the French chemist and biologist Louis Pasteur eventually resolved this issue. The spontaneous generation conflict Spontaneous generation – that living organisms could develop from nonliving or decomposing matter. Pasteur’s swan neck flasks used in his experiments on the spontaneous generation of microorganisms Louis Pasteur (1822 – 1895) Pasteur’s contributions: • Final refutation of spontaneous generation – birth of microbiology as a science • Discovery of the existence of anaerobic life – fermentation • Vaccines • Pasteurization Louis Pasteur working in his laboratory 1. Pasteur (1857) demonstrated that lactic acid fermentation is due to the activity of microorganisms. 2. Pasteur (1861) conflict over spontaneous generation – birth of microbiology as a science 3. Pasteur (1881) developed anthrax vaccine 4. Pasteurization Robert Koch (1843 – 1910) The recognition of microbial role in disease Robert Koch in his laboratory Koch’s postulates 1. The microorganisms must be present in every case of the disease but absent from healthy organisms. 2. The suspected microorganisms must be isolated and grown in a pure culture. 3. The disease must result when the isolated microorganisms is inoculated into a healthy host. 4. The same microorganisms must be isolated again from the diseased host The Golden age of microbiology • Koch and pure cultures • Fermentation and Pasteurization • Germ theory of desease • Vaccination Koch’s other contributions (1) • Development of pure culture technique 纯培养技术 – Potato slice – Solid medium with gelatin明胶培养基 – Solid medium with agar琼脂培养基 Koch’s other contributions (2) • Demonstration of causal agent of tuberculosis 肺结核 – Koch’s methods (developed by himself) • Microscopy • Differential staining鉴别染色法 of bacteria and human tissues • Pure culture isolation of bacteria • Animal inoculation – Received Nobel Prize for Physiology or Medicine in 1905 Other contributors with their important achievements during this experiment period are outlined as to milestones below. John Tyndall (1820-1893), the English physicist, demonstrated (1877) that dust did carry microbes and that if dust was absent the broth remained sterile even if it was directly exposed to air. Tyndall also provided evidence for the existence of heatresistant forms of bacteria. Ferdinand Cohn (1828-1898), the German botanist, found that the existence of heat-resistant form of bacterium is the bacterial endospore. Agostino Bassi (1773-1856) showed first that a silkworm disease was caused by a fungus in 1835, and also pointed out that many diseases were microbial etiology diseases. M. J. Berkeley, in 1845, had demonstrated that the great Potato Blight of Ireland was caused by a fungus. This event has been mentioned earlier in this chapter. Joseph Lister (1827-1912), an English surgeon, developed a system of surgery designed to prevent microorganisms from entering wounds based on the germ theory of disease. His patients had fewer postoperative infections, which indirectly proved that microorganisms were the causal agents of human disease. He published his findings in1867, thereby transformed the practice of surgery. Sergei Winogradsky (1856-1953), a Russian microbiologist, contributed many discoveries in soil bacteria. He demonstrated that bacteria could oxidize iron, sulfur, and ammonia to obtain energy. He also isolated anaerobic nitrogen-fixation bacteria from soil and studied cellulose decomposition. Martinus Beijerinck (1851-1931), the Dutch microbiologist, successfully isolated aerobic nitrogen-fixing bacterium-a root nodule bacterium Rhizobium and sulfate reducing bacteria. He also made many achievements in microbial ecology and other fields such as the developments of enrichment cultures and selective media with his associate Winogradsky. The discovery of microbial effects on organic and inorganic matter The Russian microbiologist Winogradsky discovered that soil bacteria could oxidize iron, sulfur and ammonia to obtain energy, and also isolated nitrogen – fixing bacteria. Beijerinck made fundamental contributions to microbial ecology. He isolated Azotobacter and Rhizobium. Beijerinck and Winogradsky are respected as pioneers of soil microbiology. Microbiology in the Twentieth Century Achievements accumulated during the Experiment period laid the solid foundations for the rapid development of microbiology as the coming of Twentieth Century. The first half of the century could be regarded as a developmental period and the second half should be matured or update period. New branches of microbiology were set up and developed including microbial genetics, immunology, virology and molecular microbiology, particularly the technology of recombinant DNA, which renewed the research and practical applications in all fields of biological science. Some monumental achievements are illustrated below giving an overview on the developments of microbiology in this century. Date Contributors 1909 Howard Ricketts 1910 Paul Ehrlich 1928 Frederick Griffith Discovered bacterial transformation 1929 Alexander Fleming Discovered penicillin 1933 Ernst Ruska Designed the first transmission electron microscope 1935 Wendell Stanley 1941 George W. Beadle & Edward L. Tatum Salvadore Luria & Max Delbruck 1943 Achievements T. First observed rickettsia bodies in a case of Rocky Mountain Spotted Fever and demonstrated that the disease was transmitted by the wood tick. First synthesized chemotherapeutic agent for syphilis M. Purified and crystallized tobacco mosaic virus Studied the relationship between genes and enzymes using the bread mold, Neurospora. Raised the hypothesis of one-geneone-enzyme. Showed that the mutations were spontaneous and not directed by the environment employing the fluctuation analysis. 1944 Oswald T. Avery, Provided evidence that deoxyribonucleic acid (DNA) was the Colin M. genetic material and carried genetic information during MacLeod, & transformation. Maclyn McCarty 1946 Joshua Lederberg & Edward Tatum Discovered the bacterial conjugation. L. 1949 John Enders, Successfully cultured poliovirus in human tissue cultures. Thomas H. Weller, & Frederick C. Robbins 1952 A. D. Hershey & M. Chase. J. Lederberg Norton Zinder & J. Lederberg 1953 Showed that bacteriophages inject DNA into host cells. Developed replica plating analysis. Discovered generalized tranduction. James D. Watson Identified the physical double helix structure of DNA & Frances H C. Crick Discovered the immune tolerance. P B. Medawar 1955 Francois Jacob Discovered the F factor is a plasmid. & Wollman 1956 Umbarger 1961 F. Jacob, J Propose the operon model of gene regulation. Monod & Andre Lwoff 19611966 Robert Holley, Elucidate the genetic code for amino acids. H G. Khorana & M W. Nirenberg 1969 Gerald Edelman, Rodney Porter Discovered the feedback repression. M, Described the nature and structure of antibodies. & R. 19701972 1973 Daniel Nathans Hamilton Smith & Werner Arber Renato Dulbecco, Haoward Temin & David Baltimore Bruce Ames Cohen & others Discovered and purified the restriction endonucleases. Discovered the reverse transcriptase in retroviruses. Developed the bacterial assay for the detection of mutagens. Use the plasmid vectors to clone genes in bacteria. 1975 Georges J.E. Developed the technique for producing monoclonal Köhler & César antibodies. Milstein 1977 Carl R. Woese Described of archaes as a distinct microbial group differ Frederick Sanger to eubacteria. & Walter Gilbert Developed the technique for DNA sequencing and sequenced the DNA of phage ØX174. 19821983 19831984 Cech & Altman Barbara McClintock Stanley B. Prusiner Gallo & Montagnier Kary B. Mullis Discovery of catalytic RNA (ribozyme). Discovery of transposons was acknowledged. Discovered prion (proteinaceous infectious particle). Isolated and identified HIV. Developed the polymerase chain reaction to multiply DNA. 1988 Johann Discovered and assayed bacterial photosynthesis pigments. Deisenhofer, Robert Huber & Hartmut Michel 1989 J. Michael Discovered cancer-causing genes called oncogenes. Bishop & Harold E. Varmus 1990 First human gene therapy testing begun. 19952000 Haemophillus influenzae genome sequenced (1995). Methanococcus jannaschii genome sequenced (1996) First eukaryottic cell yeast genome sequenced (1997). Escherichia coli genome sequenced (1997). Identified that Vibrio cholerae has two separate chromosomes (2000). Sir Alexander Fleming discovered the antibiotic penicillin. He had the insight to recognize the significance of the inhibition of bacterial growth in the vicinity of a fungal contaminant when most other scientists probably would have simply discarded the contaminated plates. Alexander Fleming (1881-1955) III. The importance and applications of microbiology Microorganisms also have many commercial applications. They are used in the synthesis of such chemical products as acetone, organic acids, enzymes, alcohols, and many drugs. The process for producing acetone and butanol by bacteria was discovered in 1914 by Chaim Weizmann, a Polish-born chemist working in England for Winston Churchill. When World War I broke out in August of that year, the production of acetone was very important for making cordite (gunpowder) for use in the manufacture of munitions. Weismann ’ s discovery played a significant role in determining the outcome of the war. After the war, Weismann refused all honors proposed by the British government. However, he did use his influence to encourage the British to help establish a Jewish homeland in Palestine. In 1949, Weismann was elected the first president of Israel. The food industry also uses microbes in producing vinegar, sauerkraut, pickles, alcoholic beverages, green olives, soy sauce, buttermilk, cheese, yogurt, and bread. In addition, bacteria and other microbes can now be manipulated to produce substances that they normally do not synthesize. Through this technology, called genetic engineering, bacteria and other microbes can produce important therapeutic substances such as insulin, human growth hormone, and interferon. Microbiology Basic microbiology According to biological problem of study microbial taxonomy microbial cytology microbial biochemistry microbial genetics microbial physiology microbial ecology immunology Applied microbiology According to object of study virology bacteriology fungus phycology protozoology According to applied field According to applied technique food microbiology industrial microbiology environmental microbiology microbial medicine pathogenic microorganism agricultural microbiology medical microbiology brewage technique fermentation engineering biological products Microbiologic test environment bioengineering genetic engineering enzyme engineering antibiotics IV. How to Study Microbiology 1.Understanding the Theme of the Course Carefully read the preface of the book and briefly scan the contents before you begin to study the subject. This will effectively help you to manage your schedule of learning microbiology. Based on the demands of the course, find out weaknesses in your former courses and considerably counteract them to ensure your success in microbiology study. 2. Using Concept-Map and Mind-Map to Study The term concept-map refers to as a learning method that sum up the concepts you have learnt in form of a map. It has been proved an effective method in either self-teaching or classroom teaching. Mind-map is also a skill of study in form of a map. Different from the concept-map, it is a reflection of your minds during the thinking processes when you are learning. It seams somewhat at will, but actually many visual aids have been employed in the process and these are effective in learning with a viewpoint of psychology. 3. Take Notes Carefully Notice that notes are not the simple copies of what showed or appeared on the screen or blackboard. They are the critical or important ideas or elucidates about the contents including some illustrations. It is important to avoid burring your head in the notebook busy on making notes. 4. Preview and Review in Time Prepare your lessons by reading the sections carefully and questioned what are the most interested and not clear. Listen carefully to the teacher for finding out the answers or extensive information closely to your interests. Further reading and visiting Internets are also effective aids in study. Review in time before you forget what you have learnt is a most effective way to remember them. The efficiency in this way may be twice or more of that reviewing when forgotten. Either concept-map or mind-map can be used as effective methods in reviewing. Find out interested topics During the studying process, try to find out the topics you interest in and make an effort to get more massages or information about them. They will bring you into the entire microbial world without a consciousness.