Shixue Yin (Prof Dr) Microbiology Section CESE, YZU, 225009 PRC1 Environmental Microbiology What can you know from the title of this course shown above?

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Shixue Yin (Prof Dr)Microbiology SectionCESE, YZU, 225009 PRC

Environmental MicrobiologyEnvironmental MicrobiologyWhat can you know from the title of this What can you know from the title of this course shown above? course shown above?

You must have already been told or leant You must have already been told or leant something about microorganisms. Tell me something about microorganisms. Tell me what are they (e. g microorganisms) all what what are they (e. g microorganisms) all what you have known.you have known.

Hints: SARS, cold, hospital, Hints: SARS, cold, hospital, skin/muscle(skin/muscle( 肌肉肌肉 ) cut, diarrhea() cut, diarrhea( 痢痢疾疾 )) size, shape…….size, shape…….

Question 1Question 1

Question 2Question 2

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Chapter 1 IntroductionChapter 1 Introduction

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What is Microbiology?What is Microbiology?

Microbiology is the study of organisms too Microbiology is the study of organisms too small to be clearly seen by the unaided eye small to be clearly seen by the unaided eye (i.e., microorganisms) and how they are (i.e., microorganisms) and how they are living/working/surviving.living/working/surviving.– Microorganisms includeMicroorganisms include

Bacteria (Bacteria ( 细菌细菌 ) 0.5~2 µm) 0.5~2 µm Archaea (Archaea ( 古菌古菌 ) 0.5~2 µm) 0.5~2 µm Fungi (Fungi ( 真菌真菌 ) 2~200 µm) 2~200 µm Protozoa (Protozoa ( 原生动物原生动物 ) mm~cm) mm~cm Algae (Algae ( 藻类藻类 ) ) Viruses (Viruses ( 病毒病毒 ) 20~300 nm) 20~300 nm

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Beside their small in size, they are:1. 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.

2. Diverse in their living habits (adaptation, live almost everywhere where life is possible

3. High metabolic activities, fast reproduction.

4. more numerous than any other kind of organisms (genetic diversity)

5. global ecosystem depends on their activities

6. 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?

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生物演化生物演化时间时间略表略表

Origin

Vertebrate脊椎动物

EukaryotesInvertebrate无脊椎动物

Dinosaurs恐龙

Human

Prokaryotes only 40 亿年

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Microbiology coversMicrobiology covers

– e.g., microbial morphologye.g., microbial morphology– e.g., microbial physiologye.g., microbial physiology– e.g., microbial geneticse.g., microbial genetics– Microbial taxonomyMicrobial taxonomy– Microbial cytologyMicrobial cytology

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Fields of MicrobiologyFields of Microbiology

Virology = Study of virusesVirology = Study of viruses Bacteriology = Study of bacteriaBacteriology = Study of bacteria Phycology = Study of algaePhycology = Study of algae Mycology = Study of fungiMycology = Study of fungi Protozoology = Study of protozoaProtozoology = Study of protozoa Food and dairy microbiologyFood and dairy microbiology Agricultural microbiologyAgricultural microbiology Microbial ecologyMicrobial ecology Medical microbiologyMedical microbiology Microbial genetics and molecular biologyMicrobial genetics and molecular biology

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Where are virus?

Current system of classificationCurrent system of classification

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What is Environmental What is Environmental Microbiology?Microbiology?

Environmental Microbiology covers the same Environmental Microbiology covers the same subjects stated in previous slide, but stresses subjects stated in previous slide, but stresses on the organisms and their roles in producing on the organisms and their roles in producing and/or eliminating environmental problems. and/or eliminating environmental problems. – Subject includesSubject includes

Biological treatment of wastes (liquid, solid, gaseous)Biological treatment of wastes (liquid, solid, gaseous) Biogeochemical roles in element cyclingBiogeochemical roles in element cycling Microbial transformation of toxic materials in environmentsMicrobial transformation of toxic materials in environments Interactions between them/other organismsInteractions between them/other organisms Microorganisms relevant to public healthMicroorganisms relevant to public health Tools and technologies to study/know themTools and technologies to study/know them

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Brief history of MicrobiologyBrief history of Microbiology

See how Microbiology as a science was See how Microbiology as a science was developed and think what we can know developed and think what we can know from the history.from the history.

1 Observation tools1 Observation tools

2 Fight against food decay and diseases2 Fight against food decay and diseases

3 From laboratory to natural environment3 From laboratory to natural environment

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Antony Van Antony Van Leeuwenhock Leeuwenhock (1632-1723) (1632-1723)

DutchDutch

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Discovery of MicroorganismsDiscovery of Microorganisms

Antony van Leeuwenhoek (1632-1723)Antony van Leeuwenhoek (1632-1723)– Built more than 500 microscopesBuilt more than 500 microscopes– first person to observe and describe first person to observe and describe

microorganisms accuratelymicroorganisms accurately– Known today as the father of Known today as the father of

protozoology and bacteriologyprotozoology and bacteriology

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First microorganism seenFirst microorganism seen

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Golden Age of MicrobiologyGolden Age of Microbiology(1857- 1914)(1857- 1914) Is spontaneous generation of microbial Is spontaneous generation of microbial

life exists?life exists? What causes fermentation?What causes fermentation? What causes diseases?What causes diseases? How can we prevent infection and How can we prevent infection and

disease?disease?

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Louis Pasteur Louis Pasteur (1822-1895)(1822-1895)

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Louis PasteurLouis Pasteur

Louis PasteurLouis Pasteur– Rejected theory of spontaneous Rejected theory of spontaneous

generation generation – demonstrated that alcohol fermentations demonstrated that alcohol fermentations

and other fermentations were the result of and other fermentations were the result of microbial activitymicrobial activity

– developed the process of pasteurization developed the process of pasteurization to preserve wine during storage by to preserve wine during storage by heating wine just enough to kill bacteriaheating wine just enough to kill bacteria

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Pasteur’s experiment with Pasteur’s experiment with the swan-necked flaskthe swan-necked flask

Nonsterile liquid poured into flaskNonsterile liquid poured into flask Neck of flask drawn out in flameNeck of flask drawn out in flame Liquid sterilized by heatingLiquid sterilized by heating Liquid cooled slowlyLiquid cooled slowly Dust and microorganisms trapeped in bendDust and microorganisms trapeped in bend Liquid remains sterile for many yearsLiquid remains sterile for many years Flask tipped so microorganisms-laden dust Flask tipped so microorganisms-laden dust

contacts sterile liquidcontacts sterile liquid Microorganisms grow in liquidMicroorganisms grow in liquid

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Swan-Swan-necked necked flaskflask

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Tyndall’s Dust-Free Box

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Joseph Lister Joseph Lister (1827-1912)(1827-1912)

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Joseph Lister (1827-1912)Joseph Lister (1827-1912)

Developed a system of antiseptic (Developed a system of antiseptic ( 无无菌菌 ) surgery () surgery ( 外科手术外科手术 ) designed to ) designed to prevent microorganisms from entering prevent microorganisms from entering woundswounds– Surgical instruments were heat sterilizedSurgical instruments were heat sterilized– Phenol prevented wound infection Phenol prevented wound infection

because it killed bacteriabecause it killed bacteria

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Robert Koch Robert Koch (1843-1910)(1843-1910)

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Recognition of the Relationship Recognition of the Relationship between Microorganisms and Diseasebetween Microorganisms and Disease

Robert Koch (1843-1910)Robert Koch (1843-1910)– established the relationship between established the relationship between

Bacillus anthracisBacillus anthracis and anthrax and anthrax– Announced that cause of tuberculosis(Announced that cause of tuberculosis( 肺肺

结核结核 ) is a rod-shaped bacterium; ) is a rod-shaped bacterium; Mycobacterium tuberculosisMycobacterium tuberculosis

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One of Koch’s first micrographs One of Koch’s first micrographs showing showing Bacillus anthracisBacillus anthracis

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Koch’s postulatesKoch’s postulates

The microorganism must be present in The microorganism must be present in every case of the disease but absent from every case of the disease but absent from healthy individuals.healthy individuals.

The suspected microorganism must be The suspected microorganism must be isolated and grown in a pure culture.isolated and grown in a pure culture.

The same disease must result when the The same disease must result when the isolated microorganism is inoculated into a isolated microorganism is inoculated into a healthy host.healthy host.

The same microorganism must be isolated The same microorganism must be isolated again from the diseased host.again from the diseased host.

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Development of Techniques for Development of Techniques for Studying Microbial PathogensStudying Microbial Pathogens

Koch’s work led to discovery or Koch’s work led to discovery or development of:development of:– agaragar– petridishpetridish– nutrient broth and nutrient agarnutrient broth and nutrient agar– methods for isolating microorganismsmethods for isolating microorganisms

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Fannie Hesse suggested the use of agar Fannie Hesse suggested the use of agar as solidifying agentas solidifying agent– Agar was not attacked by bacteriaAgar was not attacked by bacteria– Did not melt until reaching a temperature of Did not melt until reaching a temperature of

100 100 00CC Richard Petri developed the petri dish, a Richard Petri developed the petri dish, a

container for solid culture media that is container for solid culture media that is currently used in every micro lab all over currently used in every micro lab all over the world.the world.

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Charles Charles Chamberland Chamberland (1851-1908)(1851-1908)

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Charles Chamberland Charles Chamberland (1851-1908)(1851-1908)

– discovered viruses and their role in discovered viruses and their role in diseasedisease

– developed porcelain bacterial filterdeveloped porcelain bacterial filter– discovered the first viral pathogen, discovered the first viral pathogen,

Tobacco Mosaic Virus TMVTobacco Mosaic Virus TMV

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Other developments…Other developments…Immunological studiesImmunological studies Pasteur and RouxPasteur and Roux

– discovered that incubation of cultures for discovered that incubation of cultures for long intervals between transfers caused long intervals between transfers caused pathogens to lose their ability to cause pathogens to lose their ability to cause diseasedisease

– Attenuated culture is a vaccineAttenuated culture is a vaccine Pasteur and his coworkersPasteur and his coworkers

– developed vaccines for chicken cholera(developed vaccines for chicken cholera( 霍霍乱乱 ), anthrax(), anthrax( 炭疽炭疽 ), and rabies(), and rabies( 狂犬病狂犬病 ))

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More developments…More developments…

Emil von Behring (1854-1917) and Emil von Behring (1854-1917) and Shibasaburo Kitasato (1852-1931)Shibasaburo Kitasato (1852-1931)– developed antitoxins for diphtheria and tetanusdeveloped antitoxins for diphtheria and tetanus– evidence for humoral immunityevidence for humoral immunity

Elie Metchnikoff (1845-1916)Elie Metchnikoff (1845-1916)– discovered bacteria-engulfing, phagocytic cells in discovered bacteria-engulfing, phagocytic cells in

the bloodthe blood– evidence for cellular immunityevidence for cellular immunity

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– extremely important conceptual development in microbiology (and in microbial ecology, too)

remove organisms from complex communitiesisolate key processesobtain reproducible resultsThis method is still used today

Attitude of Koch’s time:

“Work with impure cultures yields nothing but nonsense andPenicillium glaucum“ (Oscar Brefield 1881)

Pure Culture Paradigm (Pure Culture Paradigm ( 范例范例 ))

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Sir Alexander Fleming (1929), examining exactly such an impure culture (Staphylococcus culture contaminated by

Penicillium), led to the discovery of penicillin.

Agar petri dish

Staphylococcus

colonies

Penicillium contaminant

zone of no bacterial growth, due to penicillin produced by fungus

Interference competition!classic ecological process

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Shixue Yin (Prof Dr)Microbiology SectionCESE, YZU, 225009 PRC Sergei Winogradsky Sergei Winogradsky

(A Russian microbiologist (A Russian microbiologist 1856-1953)1856-1953)

Bacteria: central in elementtransformations

Founder of soil microbiology

- 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

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Martinus Beijerinck (1851-Martinus Beijerinck (1851-1931) 1931)

“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 SchoolOf Microbiology

A Dutch microbiologist

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Martinus Beijerinck (1851-1931)Martinus Beijerinck (1851-1931)

isolated N fixers and S reducersisolated N fixers and S reducers

‘‘microbial ubiquity’: all microorganisms are everywhere; microbial ubiquity’: all microorganisms are everywhere; conditions and resources determine who flourishesconditions and resources determine who flourishes

enrichment culture: growth medium tailored to suit enrichment culture: growth medium tailored to suit particular metabolic functionparticular metabolic function

with Winogradsky, recognized that microbes are the major with Winogradsky, recognized that microbes are the major players in element transformationsplayers in element transformations

led to field of global biogeochemistryled to field of global biogeochemistry

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Albert Jan Kluyver (1888-1956)Albert Jan Kluyver (1888-1956)

-student of Beijerinck

-microbial physiology

-comparative approach

-unifying metabolic features among microbes

-leader of the Dutch school

after Beijerinckmicrobial physiology comparative approach

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Shixue Yin (Prof Dr)Microbiology SectionCESE, YZU, 225009 PRC Cornelius Bernardus van Niel Cornelius Bernardus van Niel

(1897-1985)(1897-1985)

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-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)

Cornelius Bernardus van Niel Cornelius Bernardus van Niel (1897-1985)(1897-1985)

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Shixue Yin (Prof Dr)Microbiology SectionCESE, YZU, 225009 PRC Robert E. Hungate Robert E. Hungate

(1908-2004)(1908-2004)

AKA “Grampa Bob”Anaerobic methodsCows and termites

-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

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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.

double-helix structure of DNA

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Frederick Sanger developed a method to sequence DNA in 1977. He and his co-workers Paul Berg and Walter Gilbert received the Nobel Prize in Chemistry in 1980

Frederick Sanger Walter Gilbert Paul Berg

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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.

Bacteria

Archaea Eukarya

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Kary B. Mullis Michael Smith

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

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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.

Genomic Sequence: Contribution from The Institute for Genomic Research (TIGR)

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• 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.

Genomic Sequence: Contribution from The Institute for Genomic Research (TIGR)

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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

Other Contributions

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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

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In the future In the future microbiologists will bemicrobiologists will be

Trying to better understand and control Trying to better understand and control existing, emerging, and reemerging existing, emerging, and reemerging infectious diseases infectious diseases

Studying the association between infectious Studying the association between infectious agents and chronic diseases agents and chronic diseases

Learning more about host defenses and Learning more about host defenses and host-pathogen interactions host-pathogen interactions

Developing new uses for microbes in Developing new uses for microbes in industry, agriculture, and environmental industry, agriculture, and environmental control control

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Still discovering the many microbes Still discovering the many microbes that have not yet been identified and that have not yet been identified and cultured cultured

Trying to better understand how Trying to better understand how microbes interact and communicate microbes interact and communicate

Analyzing and interpreting the ever-Analyzing and interpreting the ever-increasing amount of data from increasing amount of data from genome studies genome studies

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Fields of MicrobiologyFields of Microbiology

Microbial ecology-Environmental Microbial ecology-Environmental microbiologymicrobiology

Medical microbiologyMedical microbiology Microbial genetics and molecular Microbial genetics and molecular

biology biology

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Shixue Yin (Prof Dr)Microbiology SectionCESE, YZU, 225009 PRC Summary of this

chapter1.What is microorganisms, microbiology, environmental microbiology?

2.Characteristics of microorganisms

3.Three domains of life

4.Scope of microbiology

5.Brief history of microbiology (try to remember a few important events and heroes involved, e. g. Louis Pasteur, Robert Koch ……)

6.Future trends of microbiology (molecular)Can you image what will be taught in this subject???

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After Introduction, can you image what will be taught in this subject ??? This question speaks itself why we say so much in this first class.

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Shixue Yin (Prof Dr) Microbiology Section CESE, YZU, 225009 PRC1 Environmental Microbiology What can you know from the title of this course shown above?