Environmental Microbiology

1. Environmental Microbiology Question 1 Question 2 What can you know from the title of this course shown above? You must have already been told or leant something about microorganisms. Tell me what are they (e. g microorganisms) all what you have known. Hints: SARS, cold, hospital, skin/muscle(肌肉) cut, diarrhea(痢疾) size, shape…….

2. Chapter 1 Introduction

3. What is Microbiology? • Microbiology is the study of organisms too small to be clearly seen by the unaided eye (i.e., microorganisms) and how they are living/working/surviving. • Microorganisms include • Bacteria (细菌) 0.5~2 µm • Archaea (古菌) 0.5~2 µm • Fungi (真菌) 2~200 µm • Protozoa (原生动物) mm~cm • Algae (藻类) • Viruses (病毒) 20~300 nm

4. Beside their small in size, they are: • Basically unicellular, their life dose not depend on other cells. It means that ONE cell is a complete life, which distinguishes from other multicultural organisms. • Diverse in their living habits (adaptation, live almost everywhere where life is possible • High metabolic activities, fast reproduction. • more numerous than any other kind of organisms (genetic diversity) • global ecosystem depends on their activities • influence human society in many ways • Microorganisms are thought to have been living on the earth for 2.3~4.7 billion years. • How many years have human beings been living on the earth?

5. 生物演化时间略表 Vertebrate脊椎动物 Invertebrate无脊椎动物 Origin Prokaryotes only Eukaryotes 40亿年 Dinosaurs恐龙 Human

6. Microbiology covers • e.g., microbial morphology • e.g., microbial physiology • e.g., microbial genetics • Microbial taxonomy • Microbial cytology

7. Fields of Microbiology • Virology = Study of viruses • Bacteriology = Study of bacteria • Phycology = Study of algae • Mycology = Study of fungi • Protozoology = Study of protozoa • Food and dairy microbiology • Agricultural microbiology • Microbial ecology • Medical microbiology • Microbial genetics and molecular biology

8. Current system of classification Where are virus?

9. What is Environmental Microbiology? • Environmental Microbiology covers the same subjects stated in previous slide, but stresses on the organisms and their roles in producing and/or eliminating environmental problems. • Subject includes • Biological treatment of wastes (liquid, solid, gaseous) • Biogeochemical roles in element cycling • Microbial transformation of toxic materials in environments • Interactions between them/other organisms • Microorganisms relevant to public health • Tools and technologies to study/know them

10. Brief history of Microbiology See how Microbiology as a science was developed and think what we can know from the history. 1 Observation tools 2 Fight against food decay and diseases 3 From laboratory to natural environment

11. Antony Van Leeuwenhock (1632-1723) Dutch

12. Discovery of Microorganisms • Antony van Leeuwenhoek (1632-1723) • Built more than 500 microscopes • first person to observe and describe microorganisms accurately • Known today as the father of protozoology and bacteriology

14. First microorganism seen

15. Golden Age of Microbiology(1857- 1914) • Is spontaneous generation of microbial life exists? • What causes fermentation? • What causes diseases? • How can we prevent infection and disease?

16. Louis Pasteur (1822-1895)

17. Louis Pasteur • Louis Pasteur • Rejected theory of spontaneous generation • demonstrated that alcohol fermentations and other fermentations were the result of microbial activity • developed the process of pasteurization to preserve wine during storage by heating wine just enough to kill bacteria

18. Pasteur’s experiment with the swan-necked flask • Nonsterile liquid poured into flask • Neck of flask drawn out in flame • Liquid sterilized by heating • Liquid cooled slowly • Dust and microorganisms trapeped in bend • Liquid remains sterile for many years • Flask tipped so microorganisms-laden dust contacts sterile liquid • Microorganisms grow in liquid

19. Swan-necked flask

20. Tyndall’s Dust-Free Box

21. Joseph Lister (1827-1912)

22. Joseph Lister (1827-1912) • Developed a system of antiseptic (无菌) surgery (外科手术) designed to prevent microorganisms from entering wounds • Surgical instruments were heat sterilized • Phenol prevented wound infection because it killed bacteria

23. Robert Koch (1843-1910)

24. Recognition of the Relationship between Microorganisms and Disease • Robert Koch (1843-1910) • established the relationship between Bacillus anthracis and anthrax • Announced that cause of tuberculosis(肺结核) is a rod-shaped bacterium; Mycobacterium tuberculosis

25. One of Koch’s first micrographs showing Bacillus anthracis

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

27. Development of Techniques for Studying Microbial Pathogens • Koch’s work led to discovery or development of: • agar • petridish • nutrient broth and nutrient agar • methods for isolating microorganisms

28. Fannie Hesse suggested the use of agar as solidifying agent • Agar was not attacked by bacteria • Did not melt until reaching a temperature of 100 0C • Richard Petri developed the petri dish, a container for solid culture media that is currently used in every micro lab all over the world.

29. Charles Chamberland (1851-1908)

30. Charles Chamberland (1851-1908) • discovered viruses and their role in disease • developed porcelain bacterial filter • discovered the first viral pathogen, Tobacco Mosaic Virus TMV

31. Other developments…Immunological studies • Pasteur and Roux • discovered that incubation of cultures for long intervals between transfers caused pathogens to lose their ability to cause disease • Attenuated culture is a vaccine • Pasteur and his coworkers • developed vaccines for chicken cholera(霍乱), anthrax(炭疽), and rabies(狂犬病)

32. More developments… • Emil von Behring (1854-1917) and Shibasaburo Kitasato (1852-1931) • developed antitoxins for diphtheria and tetanus • evidence for humoral immunity • Elie Metchnikoff (1845-1916) • discovered bacteria-engulfing, phagocytic cells in the blood • evidence for cellular immunity

33. Pure Culture Paradigm (范例) – extremely important conceptual development in microbiology (and in microbial ecology, too) remove organisms from complex communities isolate key processes obtain reproducible results This method is still used today Attitude of Koch’s time: “Work with impure cultures yields nothing but nonsense and Penicillium glaucum“ (Oscar Brefield 1881)

34. Sir Alexander Fleming (1929), examining exactly such an impure culture (Staphylococcus culture contaminated by Penicillium), led to the discovery of penicillin. zone of no bacterial growth, due to penicillin produced by fungus Agar petri dish Staphylococcus colonies Penicillium contaminant Interference competition! classic ecological process

35. Sergei Winogradsky (A Russian microbiologist 1856-1953) • - isolated nitrifying bacteria • winogradsky column: microbial communities develop along a gradient of oxygen tension; method still used today • - described oxidation of hydrogen sulfide, sulfur, ferrous iron • - …all leading to the concept of chemoautotrophy – deriving energy from chemical oxidation of inorganic compounds and carbon from CO2 Bacteria: central in element transformations Founder of soil microbiology

36. Martinus Beijerinck (1851-1931) A Dutch microbiologist “The way I approach microbiology...can be concisely stated as the study of microbial ecology, i.e., of the relation between environmental conditions and the special forms of life corresponding to them” Founder of the Dutch Delft School Of Microbiology

37. Martinus Beijerinck (1851-1931) • isolated N fixers and S reducers • ‘microbial ubiquity’: all microorganisms are everywhere; conditions and resources determine who flourishes • enrichment culture: growth medium tailored to suit particular metabolic function • with Winogradsky, recognized that microbes are the major players in element transformations • led to field of global biogeochemistry

38. Albert Jan Kluyver (1888-1956) • student of Beijerinck • microbial physiology • comparative approach • unifying metabolic features among microbes • leader of the Dutch school after Beijerinck microbial physiology comparative approach

39. Cornelius Bernardus van Niel (1897-1985)

40. Cornelius Bernardus van Niel (1897-1985) • Isolated purple sulfur bacteria • Major contribution, chemistry of photosynthesis: • 2 H2A + CO2 CH2O + 2 A + H2O • where A can be Sulfur or Oxygen… • extended model to photosynthesis in green plants • oxygen from water, not from CO2 • Also, chemistry of denitrification, definition of prokaryote in 1961 (with R. Stanier)

41. Robert E. Hungate (1908-2004) • student of van Niel • methods for isolating anaerobes • culture methods – select using natural substrates, rather than guesses about what organisms eat • microbiology of guts of rumen, termites • ASM president when “Environmental Microbiology” and “Microbial Ecology” formally recognized AKA “Grampa Bob” Anaerobic methodsCows and termites

42. double-helix structure of DNA In 1953 James Watson and Francis Crick publish a description of the double-helix structure of DNA. The paper acknowledges that the authors were "stimulated by knowledge of the unpublished experimental results of" Maurice Wilkins and Rosalind Franklin, whose x-ray crystallography images of DNA suggested the structure. Franklin died in 1958; Watson, Crick and Wilkins are awarded the Nobel Prize in Physiology or Medicine in 1962.

43. Paul Berg Walter Gilbert Frederick Sanger

44. Eukarya Archaea Bacteria Carl Woese uses ribosomal RNA analysis to identify a third form of life, the Archea, whose genetic makeup is distinct from but related to both Bacteria and Eucaryea.

45. Kary B. Mullis invented the polymerase chain reaction (PCR) method in 1983. He and Kary B. Mullis received The Nobel Prize in Chemistry 1993 Kary B. Mullis Michael Smith

46. Genomic Sequence: Contribution from The Institute for Genomic Research (TIGR) The Institute for Genomic Research (TIGR) published the first full DNA sequence of a free-living organism Haemophilus influenzae in 1995, which followed up that achievement with a rapid-fire series of scientific accomplishments, including: • Deciphering the genome of the smallest bacterial genome, Mycoplasma genitalium, and investigating the minimum complement of genes required to support life. • Sequencing the first complete genome from a representative of the third domain of life, the Archaea. • Playing a key role in deciphering the DNA sequence of Arabidopsis thaliana, the first plant genome completed, as well as the sequences of rice and other important crops.

47. Genomic Sequence: Contribution from The Institute for Genomic Research (TIGR) • Deciphering the genome sequences of more than three dozen human pathogens, including the bacteria that cause pneumonia (肺炎), cholera(霍乱), syphilis(梅毒), meningitis(脑膜炎), Lyme disease anthrax(炭疽热)and gingivitis(齿龈炎)as well as the parasites that cause malaria(疟疾), amoebic dysentery (阿米巴痢疾), and African Sleeping Sickness (非洲昏睡病). • Finding new ways to use genomics as a tool for microbial forensics (毒物)and demonstrating the potential to use microarray technology for tumor diagnosis. • Developing a host of software tools that are widely disseminated in the scientific community to assemble, annotate and compare genomes.

48. Other Contributions 1960s: Ronald Atlas, Richard Bartha - studies of petroleum degradation - led to new field of bioremediation, - extended to many other pollutants: DDT, PCBs, mercury, selenium, industrial solvents 1970s fuel-shortage: - shortage in N fertilizer - sparked interest in the biology of nitrogen fixers

49. Current trends in Environmental microbiology: A. space exploration – microbes in extreme environments (hot springs, thermal vents, lithosphere) B. molecular techniques – diversity of microorganisms (Carl Woese), new methods to assess presence/abundance of individual species in situ C. realization that with pure culture/enrichment techniques, we know somewhere between 1-10% of existing microbial species – lots to learn! D. biology of climate change, global biogeochemistry

50. In the future microbiologists will be Trying to better understand and control existing, emerging, and reemerging infectious diseases Studying the association between infectious agents and chronic diseases Learning more about host defenses and host-pathogen interactions Developing new uses for microbes in industry, agriculture, and environmental control