Environmental Engineering Microbiology
Transcript of Environmental Engineering Microbiology
Environmental Engineering Microbiology
Ren Yuan
Office: B4-404, Lab: B4-444
Chapters Lectures
6
5
2
4
3
1
Teaching plan
2.5 credits from
32 hours in theoretical courses
16 hours in experimental courses (4 experiments)
Final marks includes:
Final exam 40%
Midterm exam 25%
Homework 15%
Quiz/Class participation/presentation 15%
Preview 5%
Evaluation Preview (课前)
0.5 point for 1 preview, total 5 points
Including:
Keywords;
7-8 pages of key
courseware
About 5-10 mins
Evaluation of Quiz/participation/presentation
(课中)
1.Participation: Interaction 1 points
2.Quiz: Yuketang and paper task 6 points
3.Presentation: 8 points
Content integrity 3 points
PPT format / layout 2 points
Time control 1 points
Team cooperation 1 point
Language fluency 1 point
Evaluation of Homework (课后)
1. Questions
2. Calculations
3. Reading and answering questions
4. Watching videos and answering questions
5. Search the information from database or internet and
summarize the main content
1.5 point for 1 homework, total 15 points
Hand in next class!
Microorganism
Good or Bad?
Discussion:
Tell your members the benefit or harm of the
microorganisms to human being, animals, fish, or
ecosystem, including their genus or names if possible.
Write down your answers. Chinese is ok.
Actually,
• 1% harm to human being
• 4% harm to animal and plant
• 95% good for us
• Decomposition of organic substances
• Agents of nutrient cycling (C, N, S, P, etc.)
• Fundamental roles in soil aggregation
• Some are beneficial for plant growth
• Photosynthesis/fix carbon
• Cause disease
What Can/Do Microbes Do?
Why this course in microbiology?
• Application of microbiology specifically to
the environment
- what is the role that microbes have on the
environment? – cycling of elements on earth,
role in water, wastewater, and geobiochemistry
- develop an understanding well enough
to use them beneficially
- kill pathogenic bacteria to keep healthy
Part 1: Review of Basic
Microbiology Concepts
• Microorganisms
• Bacterial Growth
Lecture 1: Microorganisms
Discovery History of Microorganisms
Antony van Leeuwenhoek
(1632-1723)
50-300 times
• Tiny
• Simple structure
Morphology
Physiology of Microorganisms
Louis Pasteur
(1822-1895)
Robert Koch
(1843-1910)
• Developed the process of pasteurization
• Infectious disease was caused by microorganisms
• Vaccine can be made from germs
• Established the basic operation for microorganisms
experiment (pure culture, culture medium and stain)
• Identified many kinds of pathogens
• Awarded Nobel Prize in Physiology or Medicine(1905)
Build in 1887;
24 branches all
over the world
Molecular biology
Francis H C Crick James D Watson
(1916-2004) (1928-)
Search the information after class:
• Story about the DNA discovery
• Contribution of Rosalind E Franklin
Awarded Nobel Prize in
Physiology or Medicine(1962)
Microbiology
Morphology
Physiology
Modern Microbiology
Infectious disease
Immunology
genetics
......
Applied Microbiology Soil Microbiology
Environmental Engineering
Microbiology
1 Microorganisms and human origin
Early Earth
• Formed 4.5 billion years ago
• Hot inside and cold outside
• “Extreme” environments
- opposite to what humans prefer
Oldest microbes?
Element collision
Organic matter aggregation
Atoms of C/H/O/N...
Organic molecules
Single cell,
multicellular organism
Cyanobateria
Evolutionary timeline
Oxygen in the Atmosphere
Banded Iron Formation, Hammerslay
Basin, Western Australia
Archaean and Proterozoic ages (2.7-1.9 billion years ago)
Cyanobacteria evolved the ability to utilize H2O as an e-donor
Iron Oxides (Fe3+)
• Fe2+ Fe3+
• Iron oxides accumulated
as banded iron formations
• Then O2 accumulated in
the atmosphere
H2O 2 H+ + ½ O2
O2 released to the
atmosphere
2 Classification of Organisms
Classification of Organisms
Archaea
Bacteria Eucarya
古生菌/古菌
真细菌 真核生物
Microorganisms Fungi (Yeast, Molds , Mushroom),
Single-cell algea, Protozoa
Non cell type (virus)
Cell type
Prokaryotes
原核生物
Common bacteria, Actinomyces,
Mycoplasma, Chlamydia, Rickettsia
Bacteria真细菌
Archaea古菌
Eucarya真核微生物
Classification of Microorganisms
Microbial taxonomy 分类法
• Classification
Domin
Kingdom
Division
Class
Order
Family
Genus
Species
域界门纲目科属种 Strain
真核域
动物界
脊索动物门哺乳纲
灵长目
人科
人属
人种
Nomenclature 命名
International nomenclature: Linnaeus binomial nomenclature
Bacillus subtilis
Genus + species (+ name and/or number)
From
structure, shape or scientist name color, shape, source, function, scientist…
All in Italic style
= B. subtilis
杆菌 枯草,微小
Examples
Penicillium notatum
Staphylococcus aureus
Candida tropicalis
Saccharomyces cerevisiae
P. notatum
S. aureus
C. tropicalis
S. cerevisiae
Microbial taxonomy 分类法
• Classification
• Nomenclature
• Identification ?
The size of microorganisms
Visibility scale Size Meters
Naked Eyes
Optical microscope
Electron microscope
Eucarya
Prokaryotes
3 Microorganisms
Bacteria
Archaea
Fungus
Protozoa
Algae
Virus…..
3.1 Eubacteria/Bacteria
Microbial morphology
Coccus and Rod
Klebsiella pneumoniae
肺炎克雷伯菌
Escherichia coli
大肠埃希菌
Staphylococcus aureus
金黄葡萄球菌
Bacillus subtilis
枯草芽孢杆菌
Staphylococcus pneumoniae
肺炎链球菌
Cryptococcus meningitis
脑膜炎球菌
Spirillum
Helicobacter pylori
幽门螺旋杆菌
Leptospira
钩端螺旋体
Bacterial cell structure
Gram stain 革兰氏染色
Cell envelope 细胞膜
Gram negative Gram positive
90%
10%
Cytoplasmic cell membrane细胞质膜
Functions of membrane
• Protection
• Keep the shape
• Mass transfer
Cytoplasm 细胞质/细胞浆
• Gel-like matrix
• Water, enzymes, nutrients, wastes, gases
• Ribosome, chromosome (nucleoid)
• Plasmid: DNA sequences
• mRNA: 50S, 30S, 16S
Glycocalyx 糖被
• Slime (or sticky) layer
• Protection
• Attachment to surfaces
• Mats and biofilms
• Bind metals
Polysaccharide, protein, and
nucleic acids (EPS, Extracellular
Polymeric Substances)
Appendage 附器
Flagellum
• Motility
• Attachment to surfaces
Fimbriae (G-)
• Biofilm formation
• Infection attachment
• Conjugation (Information transfer)
Pilus
Endospores 芽孢/内孢子
• G+ bacteria, Bacillus and Clostridium spp.
• Withstanding adverse conditions (radiation,
UV light, heat, desiccation, low nutrients
and chemical) to survive
• Remained viable even
for 100,000 years
3.2 The Archaea
• Simpler and the oldest form of life on Earth (like
cyanobacteria)
• Inhibit extreme and normal environment
• Similar to bacteria on structure and metabolism,
but similar genetic transcription and translation
to eukaryotes (fungi)
• Many are non-culturable
Some Archaean species
• Thermophiles 嗜热菌
• Haloarchaea 嗜盐古菌
• Methanogens (strict anaerobic) 产甲烷菌
- Extremely important in C-cycling in biosphere
and waste (water and solid) treatment
Archaea in the environment
Thermal spring ~160°C along
the side, too hot in the center,
Yellowstone National Park, US
Red coloration indicates microbes
growing on the ice
Hypersaline habitats for halophilic Archaea
Hutt Lagoon-Pink Lake is located in
Yallabatharra (40% salt, >50 °C), Western
Australia, Australia. With its main inlet blocked,
Hutt Lagoon is replenished via infrequent
rainfall and the meager inflow barely balances
the effects of evaporation. The main two types
of green algae in the lagoon are spurred to
create β-carotene, a reddish-orange organic
pigment that helps protect them from the
effects of intense sunlight.
Aerial view near San Francisco Bay, California,
of a series of seawater evaporating ponds
where solar salt is prepared. The red-purple
color is predominantly due to bacterioruberins
and bacteriorhodopsin in cells of
Halobacterium.
3.3 Fungi/Fungus
• Physically larger group of eucaryotes
• Identification:
7% of 1.5 million fungal species are estimated
morphology, spore structure
membrane fatty acid, 18S rRNA
Internal transcribed spacer
• Mostly are harmless, but majority of plant pathogens
are fungi; cause human diseases
• Fermentation (foods, alcohol, medicine…)
• Excellent degraders of organic residues in soil
分子标记
Fungal structure
葡聚糖
Identification
Immunity
质膜
Chitin
Fungal Diversity
Pilobolus kleinii Dictyophora indusiata Accharomyces cerevisiae
Zygomycota Basidiomycota Ascomycota
Molds Mushrooms Yeast
3.4 Protozoa
Cryptosporidium Ciliophora Sarcodina
• Freshwater, marine habitats, moist soils and
gastrointestinal tracts of animals (parasites)
• Serve as the food chain foundation in aquatic ecosystems
• Eat organic residues in soils as well as other soil microbes
• Size from 2-3 μm to 7 cm
Roles of Protozoa in Environmental
Microbiology
• Population control (quantity and composition) through
the predation of bacteria, algae, and even other protozoa
• Human and vertebrate parasites, food-borne and water-
borne disease
• Important role in nutrient cycling, especially in the
rhizoshphere (root zone)
• Degradation of complex organic material and polymers,
such as cellulose
NH4+, PO4
=, etc.
Soil protozoa eat bacteria
and release the nutrients
“tied up” in them.
Bacteria
Bacteria
are digested
Bacteria are
engulfed by
the amoeba
3.5 Algae
• Contain chlorophyll a,b,c, or d
• Wide range of habitats
• Physiological and
ecological considerations - Oxygenic photosynthesis
- Nitrogen fixation
- Toxin (secondary metabolisms)
Eutrophication Excess multiplication
of Algae
Excess of N and P
3.6 Virus
Comparative sizes of selected
bacteria, viruses, and nucleic acids
No metabolic capability, rely on
host metabolism
10’s to100’s of nm
Infect plant, animals, bacteria, fungi
and cause diseases
Generally species-specific
Do you know viruses?
Influenza Ebola AIDS
Bird flu Black Death Smallpox
COVID-19
Coronavirus Disease 2019
https://abcnews.go.com/Health/video/c
oronavirus-explained-69509720
Group work: Words organization
① Those bacteria that have been cultured can be
structurally separated into two major groups based on
their cell envelope architecture: gram-positive or gram-
negative.
② Cell replication and protein synthesis is centered in the
cell cytoplasm, a complex gel-like matrix composed of
water, enzymes, nutrients, wastes, and gases.
③ Archaea are microbes that look somewhat similar to
bacteria in size and shape under the light microscope
but they are actually genetically and biochemically quite
different.
④ Viruses are a group of biological entities consisting of a nucleic acid
encapsulated within a protein coat known as the capsid in various
different sizes.
⑤ The 18S rRNA based classification being used for eucaryotic
microorganisms has revealed fundamental genetic differences among
the protozoa.
⑥ Some gram-positive bacteria produce endospores capable of
withstanding adverse conditions including radiation, UV light, heat,
desiccation, low nutrients, and chemicals.
⑦ The relative importance of these DNA transfer mechanisms is still not
known but all have been shown to occur in the environment.
⑧ Many fungi secrete extracellular enzymes to break down complex
polymers to simple carbon compounds for cell utilization.
Summary
• Founders of the microbiology
• Classification of organisms
• Nomenclature of organisms
• Structure of bacteria, archaea, fungi,
protozoa, algae, and viruses
• Gram stain
Homework 1
• How many and what is the classification levels for living
things?
• How can you classify the microorganisms?
• How can you identify bacteria and fungi? (distinguish
16S and 18S rRNA)
• Search the story of Rosalind Franklin and Radical
speech of Watson.
• Search the information about “Coronavirus”:
classification, discovery, source, widespread pathway,
living environment, prevention control, vaccine, etc.