1. 1 ENVIRONMENTAL MICROBIOLOGY LECTURE # 1 Dr. Paul KONKUK UNIVERSITY DEPT. OF ENVIRONMENTAL ENGINEERING - Introduction & History

2. 2 Introducing my class I expect the class to be interactive The subject is basically very interesting if you are attentive to the class If you have not understood anything while lecturing, you can stop me and request for clarification Language (English) efficiency is NOT a parameter for evaluation I am ready to repeat if you have not understood You are encouraged to take notes while lecturing The laboratory also is equally important At the end of semester I shall help you to revise the course and prepare for the exam Assignments are very important and should be submitted within a week I will be available in my office for any clarifications regarding the chapters, upon appointment over e-mail (dibypaul@konkuk.ac.kr)/Phone (450-3318)

3. 3 Preparing your assignments COVER PAGE – Introduction Subheadings Summary Reference Page Number TITLE OF ESSAY Your name Your Number MAJOR Date Prof. Name Font Style: Times New Roman Font size : 12 Line space: 1.5

4. 4 Reference Style: JOURNAL Paul, D., Kumar, S. and Nair, S. (2005) Osmotolerance in biocontrol strain of Pseudomonas pseudoalcaligenes MSP- 538: A study using osmolyte, protein and gene expression profiling. Annals of Microbiology. 55(4) 243-247. BOOK Okuda, M and Okuda, D. (1993) Star Trek Chronology: The History of the Future. (1 st Ed). New York: Pocket Books WEB SITE http://www.bradley.edu/campusorg/psiphi/DS9/ep/503r.htm. JOURNAL ARTICLE ON THE INTERNET McCoy, L.H. (1999). Respiratory changes in Vulcans during pon farr. J Extr Med [serial online]. 47:237-247. Available at: http://infotrac.galegroup.com/itweb/nysl_li_liu.

5. 5 InstructorAsst. Prof. Diby Paul Office RoomSocial Sciences Building, Room # 528 Telephone02-450-3318 E-Maildibypaul@konkuk.ac.kr Lecture Schedule Thursday, 13.00 – 18.00 Lecture RoomB 567 Laboratory Room ………………..You can send me mail in Hangul also…………… Lecture materials will be available at: http://envtech.konkuk.ac.kr/

6. 6 DESCRIPTION AND OBJECTIVE OF THE COURSE Historically Environmental Microbiology can be traced to studies of municipal waste treatment and disposal. More recently the area has expanded to the study of soil, water and air systems, including the interaction of indigenous microbes with organic and inorganic pollutants, as well as the behavior of pathogens introduced in to these systems, thus making the field extremely important for an environmental engineer. The topics covered in this course will be Microbial Ecology, Use of microbes for waste water treatment and bioremediation, Pathogenic microorganism, Disinfection techniques etc. The students will have hands on experience in aseptic techniques, cultivation of microorganisms and experiments in biogeochemical cycling.

7. 7 REFERENCES Environmental Microbiology (2000). Academic Press. Maier, R. M. et al. Microbiology (1999). McGraw Hill. Prescott, L. et al. Brock Biology of Microorganisms (2000). 9th Ed. Madigan et al.

8. 8 SYLLABUS 1 Introduction to Environmental Microbiology, History of Microbiology 2 Microorganisms in the Environment, Structure of microorganisms 3 Microbial Ecology - Terrestrial Microbiology, Aero-microbiology, Aquatic Microbiology, Extreme environments and microbial adaptations 4Microbial Growth & Nutrition 5Laboratory experiments 6Biological molecules 7MID TERM EXAM

9. 9 SYLLABUS 8 Environmental sample collection and processing, Indicator Microorganisms 9Laboratory experiments 10Biogeochemical cycling 11 Environmental Consequences of Microbially mediated Biogeochemical cycling 12Pathogenic and Beneficial microbes in agriculture 13Laboratory experiments 14FINAL EXAM

10. 10 GRADING & EXAMS Attendance – 10% Quiz & Assignments – 25% Mid term Exam – 30% Final Exam – 35%

11. 11 Introduction to Environmental Microbiology History of Microbiology CONTENTS Lecture-1 March, 6

12. 12 VIDEO

13. 13 INTRODUCTION TO ENVIRONMENTAL MICROBIOLOGY

14. 14 MICROBIOLOGY – Study of the organisms and agents too small to be seen clearly by the unaided eye. BACTERIA, FUNGUS, VIRUSES, PROTOZOANS………

15. 15 Microbial Diversity Many years of evolution have created a stunning diversity of microbes More than one million species of bacteria suspected to exist Only about 4200 species of bacteria are described till now It is estimated that we know less than 1% of the microbial species on Earth.

16. 16 Environmental Microbiology Soil Microbiology Hazardous waste bioremediation Industrial Microbiology Food safety Diseases/Health Biotechnology Waste management Aquatic microbiology Aeromicrobiology Why Environmental Microbiology is important for Environmental Engineers?

17. 17 MICROORGANISMS are present everywhere in the nature Microbes inhabit from 20 miles beneath the Earth's surface to 20 miles overhead. They live at temperatures less than -20 O C to temperatures hotter than boiling point. Microbes thrive on a huge range of foods including oil and toxic wastes. Where do they live??

18. 18 Most animals interact with microbes in important ways, and all animals, as well as all plants depend on microbes for their survival. MICROBES vs ANIMALS Many foods, including cheese, chocolate, bread, beer, and many others are processed by microbes MICROBES vs FOOD MICROBES in SPACE ---- extra terrestrial life Microbes are found in abundance in many aquatic environments, such as streams, puddles, ponds, lakes, rivers, swamps, oceans and seas. MICROBES in WATER Their associations

19. 19 each gram of soil may contain 10,000 different species of microorganisms! MICROBES - SOIL - PLANTS Microbes as disease causing organisms in plants Fungal Bacterial Viral Colletotricum orbiculare – cucumber Xanthomonas oryzae – bacterial blight of rice CMV – cucumber - mosaic

20. 20 Tomato – leaf curl virus

21. 21 COMPOST Microbes convert organic material and these into humus by a process known as biodegradation some compost piles get so hot that they give off steam!!! The microbes that live in hot compost piles are heat lovers called "Thermophiles." Fungi Fungi are important in the composting process. Many fungi can break down the cellulose in leaves, degrade wood, which is made of large, complex molecules called lignins. This fungus is growing on a rotting wood stump.

22. 22 Plastic Eating Microbes? Can any plastic items be turned into compost? It depends on the type of plastic Most human made (synthetic) plastics are NOT biodegradable Styrofoam is a type of plastic. No microbes are known that can degrade Styrofoam. Alcaligenes eutrophus This microbes makes a biodegradable plastic. This plastic is called polyhydroxybutyrate, or PHB for short

23. 23 Heat / Cold loving microbes Some microbes can survive temperatures above the boiling point. These are called thermophiles Some microbes live on snow and ice and die at room temperature. These are called psychrophiles

24. 24 Microbes and their association with animals Most animals are intimately associated with microbes. Microbes live in their guts, in their mouths, and on their skin. Microbes are important for the good health of most animals. Because many animals have more microbe cells than they have animal cells living in or on them, it is as if animals evolved as homes for microbes. Animals provide microbes with food and shelter.

25. 25 Microbes - mouth, guts, skin, arms, and feet and every where. Habitats on human body Teeth – Streptococcus - most predominant microbe in mouth convert sugars and other carbohydrates into lactic acid. This acid then dissolves tooth enamel, eventually forming a cavity. forming plaque BIOFILMS

26. 26 STOMACH – Less microbes due to low pH – but acid loving microbes Large Intestine - Human guts are hosts to many billions of microbes. Each gram from the large intestine contains up to ten trillion (10,000,000,000,000) microbes!

27. 27

28. 28 Some of the different microbes in the intestine are Lactobacillus acidophillus This is a normal, helpful inhabitant of intestines. The billions of Lactobacilli in your intestines crowd out harmful microbes so they cannot grow. This is why many travelers take capsules filled with Lactobacillus, so they don't get traveler's diarrhea. E. coli This is the most well-studied organism. It is a normal resident of your intestine and provides you with vitamin K and some of the B vitamins Propionibacterium acne normal inhabitant of skin Staphylococcus epidermidis

29. 29 RUMEN - VERY IMPORTANT ‘ROOM’ FOR ENVIRONMENTAL ENGINEERS cows, like other ruminant animals, have a special type of stomach called a rumen, which is home to billions of microbes which HELP COW TO DIGEST grass and hay. Cellulose degraders, Methanogens Methane Green house gas & major contributor to global warming

30. 30 microbes that live inside their guts digest wood wood-feeding termites digest their fiber-rich food in a highly productive manner and, consequently, emit less methane into the atmosphere than expected

31. 31 septic tank is usually an underground tank that contains billions of microbes that slowly degrades sewage.

32. 32 MICROBES IN FOOD & BEVERAGE INDUSTRY Beer Grains, such as barley, are converted to beer with the help of yeast Bread Bread is made from grains fermented with yeast. The yeast produce the gas carbon dioxide (CO2) and the alcohol ethanol (CH3-CH2-OH). The carbon dioxide gas makes the bread rise. The ethanol evaporates during baking.

33. 33 Chocolate Chocolate is prepared with the help of microbes. Chocolate comes from the seeds of cacao trees. These seeds are in a white fleshy pod. To get the seeds out of the pod, the pod is allowed to ferment with naturally occurring microbes that include yeasts and bacteria such as Lactobacilli and Acetobacter.

34. 34 Wine Fruit juice is converted to wine with the help of yeast Yoghurt is made from fermented milk. Lactobacilli convert milk to yoghurt.

35. 35 Microbes inhabit the farthest reaches of the biosphere, floating up to six miles into the atmosphere. Microbes may inhabit space beyond our world. If life exists on other planets, it is most probably microbial life.

36. 36 Microbes in water Where there is water, there are microbes. Microbes, like other living creatures, require water to live and reproduce. Freshwater ponds to salty seas with three times the salt concentration of the ocean. Microbes live in overgrown slime (biofilm) on pipes and in open oceans with few nutrients to support microbial life. Microbes thrive in aerated streams with lots of oxygen to murky bogs that have no oxygen. Microbes containing tiny magnets and microbes that shine associating with fish.

37. 37 The amount of light and oxygen change at different depths, creating different habitats for different microbes. POND green algae and cyanobacteria. This green color comes from chlorophyll, a chemical that turns solar energy into food that the microbes can use. Anoxygenic Photosynthetic Bacteria Rhodospirillum rubrum This purple bacterium contains chlorophyll a or b and requires simple organic compounds for carbon Chromatium This purple sulfur bacterium require hydrogen sulfide as an electron and hydrogen donor to make food Chlorobium This green sulfur bacteria requires sulfur to live Heterotrophs feed off of other organisms and decaying organic matter

38. 38 Deep Sea Thermal Vents Deep below the ocean suface, where there is no light, whole ecosystems with dense animal life surround hydrothermal vents. These communities are suppported by bacteria, which create food from chemicals flowing out of volcanic vents. Some of these bacteria are free living, others live together with animals is a symbiotic relationship.

39. 39 Salty Sea Many microbes cannot survive except in the presence of high concentrations of salt. These organisms are called"halophiles." Magnetotactic Bacteria Certain bacteria have tiny magnets in them. The magnets allow these magnetotactic bacteria to move along the Earth's magnetic fields. Luminescent Bacteria In ocean. These are free-living luminescent microbes. Other luminescent microbes are found as symbionts of fish. Red Tide The Red Tide is caused by billions of microscopic red algae known as dinoflagellates that bloom periodically in the ocean.

40. 40 HISTORY OF MICROBIOLOGY

41. 41 HSTORY OF MICROBIOLOGY 1546 - Fracastoro – disease was caused by invisible living creatures 1676 - Antony von Leeuwenhoek – observation though microscope – ‘animalcules’ 1688 – Francesco Redi challenged ‘SPONTANEOUS GENERATION THEORY’ ‘Living organisms could develop from non living matter’ Covered meat in container did not develop maggots Fine gauze

42. 42 Scientists believed that microbes were SPONTANEOUSLY GENERATED 1765-1776 – attacks spontaneous generation Sealed flasks containing water and seeds, after boiling for 40min did not develop any growth THE RECOGNITON OF THE MICROBIAL ROLE IN DISEASE 1835-1844 – BASSI - Germ theory of disease-Silk worm disease was due to fungal infection 1845 – Berkely –potato blight of Ireland was caused by a fungus. 1867 – Lister -Surgery using antiseptic techniques – use of phenol and heat sterilized instruments 1876 – Robert Koch - anthrax is caused by Bacillus anthracis Injected healthy mice with material from disease animal, and the mice became ill. The anthrax bacilli was cultured n beef serum. Isolated bacilli injected again to mice to develop infection.

43. 43 Koch's postulates are: The organism must be found in all animals suffering from the disease, but not in healthy animals. 1.The organism must be isolated from a diseased animal and grown in pure culture. 2.The cultured organism should cause disease when introduced into a healthy animal. 3.The organism must be reisolated from the experimentally infected animal. Koch’s assistants Fannie - developed agar Richard Petri -developed Petri dish Koch cultured bacterium in liquid and solid medium

44. 44 1881 – Pasteur - develops anthrax vaccine 1885 - Pasteur - develops rabies vaccine 1887-1890 – Winogradsky -soil microbiology 1888- Beijerinck - nitrogen fixing bacterium 1900 – Landsteiner discovers blood groups 1923-first edition of Bergey;s manual 1929- Flemming - discovers penicillin 1944 – Avery – DNA carries information during transformation 1946 – Lederberg & Tatum – bacterial conjugation 1953 – Watson & Crick - DNA double helix model 1979 –Insulin synthesized using recombinant DNA techniques 1983 – Gallo& Montagneir - HIV isolated and identified