Microbiology

1. Microbiology （微生物学） Meng Qingheng Bio-DPT. College of Life Science and Chemistry Tjnu.

3. 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 • Microbiology 6th Ed. 1996. Totora. et. • Microbiology 5th Ed. 2002. L. M. Prescott et alwww.mhhe.com / prescott5 • Lecture ：54 h

4. Contents ： I: Morphology and Anatomy II: Physiological Functions III : Diversity & Ecological activities

5. 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.

6. 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.

7. The groups include: Bacteria 细 菌 Actinomycetse 放线 菌 Mycoplasma 支原体 Procaryotes (Monera) Chlamydia 衣原体 （原核生物）（原核界） Rickettsia 立克次氏体 Cyanobacteria 蓝细菌 Yeast 酵母菌 (Fungi) Mold( mould) 霉 菌 （真菌界） Protozoa 原生动物 Eucaryotes (Protistae) Algae 藻类 （真核生物） （原生界） Viruses 病毒 ----------- Non-cellular (Vira) （非细胞生物） （病毒界）

8. 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

10. 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

11. Microbial world Organisms (living) Infectious agents (dependent-living) eukaryotes Prokaryotes (unicellular) viruses viroids prions Algae (unicellular or multicellular Fungi (unicellular or multicellular Other multicellular organisms Eubacteria Archaea Protozoa (unicellular)

12. 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.

13. 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.

14. 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

15. 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。

16. 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。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。

17. 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。

24. 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

25. The discovery of microorganisms The first person to accurately observe and describe microorganisms Antony van Leeuwenhock (1632-1723)

26. 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.

27. lens Object being viewed A drawing of one of the microscopes showing the lens a; mounting pin b; and focusing screws c and d. adjusting screws Leeuwenhoek’s drawings of bacteria from the human mouth.

28. 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.

29. 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.

30. 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

32. 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

33. 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

34. Robert Koch (1843 – 1910) The recognition of microbial role in disease Robert Koch in his laboratory

35. Koch’s postulates • The microorganisms must be present in every case of the disease but absent from healthy organisms. • The suspected microorganisms must be isolated and grown in a pure culture. • The disease must result when the isolated microorganisms is inoculated into a healthy host. • The same microorganisms must be isolated again from the diseased host

39. The Golden age of microbiology • Koch and pure cultures • Fermentation and Pasteurization • Germ theory of desease • Vaccination

40. 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

41. 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

42. 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 heat-resistant 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.

43. 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.

44. 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.

45. 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.

46. Date Contributors Achievements 1909 Howard T. Ricketts First observed rickettsia bodies in a case of Rocky Mountain Spotted Fever and demonstrated that the disease was transmitted by the wood tick. 1910 Paul Ehrlich First synthesized chemotherapeutic agent for syphilis 1928 Frederick Griffith Discovered bacterial transformation 1929 Alexander Fleming Discovered penicillin 1933 Ernst Ruska Designed the first transmission electron microscope 1935 Wendell M. Stanley Purified and crystallized tobacco mosaic virus 1941 George W. Beadle & Edward L. Tatum Studied the relationship between genes and enzymes using the bread mold, Neurospora. Raised the hypothesis of one-gene-one-enzyme. 1943 Salvadore Luria & Max Delbruck Showed that the mutations were spontaneous and not directed by the environment employing the fluctuation analysis.

47. 1944 Oswald T. Avery, Colin M. MacLeod, & Maclyn McCarty Provided evidence that deoxyribonucleic acid (DNA) was the genetic material and carried genetic information during transformation. 1946 Joshua Lederberg & Edward L. Tatum Discovered the bacterial conjugation. 1949 John Enders, Thomas H. Weller, & Frederick C. Robbins Successfully cultured poliovirus in human tissue cultures. 1952 A. D. Hershey & M. Chase. J. Lederberg Norton Zinder & J. Lederberg Showed that bacteriophages inject DNA into host cells. Developed replica plating analysis. Discovered generalized tranduction. 1953 James D. Watson & Frances H C. Crick P B. Medawar Identified the physical double helix structure of DNA Discovered the immune tolerance.

48. 1955 Francois Jacob & Wollman Discovered the F factor is a plasmid. 1956 Umbarger Discovered the feedback repression. 1961 F. Jacob, J Monod & Andre Lwoff Propose the operon model of gene regulation. 1961-1966 Robert Holley, H G. Khorana & M W. Nirenberg Elucidate the genetic code for amino acids. 1969 Gerald M, Edelman, & Rodney R. Porter Described the nature and structure of antibodies.

49. 1970-1972 Daniel Nathans Hamilton Smith & Werner Arber Renato Dulbecco, Haoward Temin & David Baltimore Discovered and purified the restriction endonucleases. Discovered the reverse transcriptase in retroviruses. 1973 Bruce Ames Cohen & others Developed the bacterial assay for the detection of mutagens. Use the plasmid vectors to clone genes in bacteria. 1975 Georges J.E. Köhler & César Milstein Developed the technique for producing monoclonal antibodies. 1977 Carl R. Woese Frederick Sanger & Walter Gilbert Described of archaes as a distinct microbial group differ to eubacteria. Developed the technique for DNA sequencing and sequenced the DNA of phage ØX174.

50. 1982-1983 Cech & Altman Barbara McClintock Stanley B. Prusiner Discovery of catalytic RNA (ribozyme). Discovery of transposons was acknowledged. Discovered prion (proteinaceous infectious particle). 1983-1984 Gallo & Montagnier Kary B. Mullis Isolated and identified HIV. Developed the polymerase chain reaction to multiply DNA. 1988 Johann Deisenhofer, Robert Huber & Hartmut Michel Discovered and assayed bacterial photosynthesis pigments. 1989 J. Michael Bishop & Harold E. Varmus Discovered cancer-causing genes called oncogenes. 1990 First human gene therapy testing begun.