Environmental Engineering Microbiology

Ren Yuan

ceyren@scut.edu.cn

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.