Environmental Microbiology & Environmental Microbiology & ChemistryChemistry

CEB 20303

Dr R.T. Bachmann

© 2010

Assessment Methods

• 40 % exam and 60 % course works (3 lab reports, 1 assignment, 1 test).

• Scheduled duration of exam: 3 hr • Lab reports will be assessed based on

following 2 sets of criteria:– Layout (Frontpage, clear logical structure of

report, labelling of figures, tables, pages) – ca. 30 %

– Report quality (Introduction, M&M, Results, Task answers, Discussion, Conclusions, References) – ca. 70 %

Teaching Schedule & Methods

• 14 x 2 hr lectures (Tue, 3-5 PM, BK2);• Laboratory (6 groups á 3 students)

A B C D E F G

Teaching Schedule & Methods

• Laboratory time table

No. TitleMONDAY (10-1PM)

FRIDAY (3-6PM)

1

Acid-base reaction (neutralisation of H2SO4) and concurrent

Cr(III) precipitation using NaOH and KOH A-C D-F

2Reaction kinetics of electrolytic Cr(VI) reduction in aqueous acidified solution. A-C D-F 

3 Microbial growth and growth monitoring methods A-C D-F 

Public holidays

15-16th February : Chinese New Year & Mid-sem break

26th February (Fri) : Prophet Muhammad’s Birthday (Maulidur Rasul)

15th April (Mon) : Declaration of Melaka as a Historical City

AssignmentReport : IndividualDeadline : 9th April 2010

Outline:• Find a journal paper investigating the treatment of polluted air, water, soil or waste (or

renewable energy) based on a bio-chemical process;• Briefly describe using your own words & references (!!) the process principle, chemical

reactions (type of reaction, kinetics), function of microorganisms in the process and biotic / abiotic factors that affect these organisms as well as analytical methods used;

• List advantages and disadvantages of the biochemical process and compare with other treatment options;

The report will be marked based oni) report layout (clear and logical structure, informative frontpage, table of content, list of

figures / tables, references, labeling of tables, figures and pages), [30 %]

ii) report quality (concise, relevant and well referenced answers to each task)

[65 %]And

iii) on-time submission of report (bonus point for on-time submission). [5 %]

Policies

• Professional behavior expected– punctual– courteous, respectful and non-distractive – TURN CELL PHONES OFF IN CLASS!

• Academic dishonesty– representing the work of others as your own will result

in a grade of 0.0 for the course. In most cases, formal disciplinary action will also be initiated

ReferencesText Books

• Sawyer C.N. & McCarty PL. (2002) Chemistry for Environmental Engineers. 5 th edition, McGraw Hill, ISBN-13: 978-0072480665.

• Stumm, W. & Morgan, J.J. (1996) Aquatic Chemistry. 3rd Ed., Wiley-Interscience, ISBN-13: 978-0471511854.

• Birkett, J. (1999) Microbiology and Chemistry for Environmental Scientists and Engineers. 1st Ed., Taylor & Francis; ISBN-13: 978-0419226802.

• Madigan, M.T., Martinko, J.M. (2006) Brock Biology of Microorganisms. Pearson Prentice Hall, 11th ed., ISBN-13: 9780131968936.

• Pelczar, M.J., Chan, E.C.S., & Krieg, N.R. (1986) Microbiology. 5 th Ed., McGraw-Hill, ISBN-13: 978-0070492349.

• Cappuccino, J.G. & Sherman, N. (1999) Microbiology : a laboratory manual. 8 th Ed., Benjamin Cummings, ISBN-13: 978-0805325782.

• Mitchell, R. (1993) Environmental Microbiology. Wiley-Liss, ISBN-13: 978-0471595878.• Maier, R.M., Pepper, I.L., Gerba, C.P. (2000) Environmental Microbiology. Academic Press, 1st

ed., ISBN-13: 978-0124975705.• Jjemba, P.K. (2004) Environmental Microbiology: Principles and Applications. Science

Publishers, ISBN-13: 978-1578083480.• Gerhardt, P., Murray, R.G.E., Wood, W.A. & Krieg, N.R. (1994) Methods of general and

molecular bacteriology. American Society for Microbiology, Washington, USA, ISBN: 1555810489

• APHA Standard method for examination of water and wastewater analysis. 20 th Ed.

References

Online references• Microscopy:

http://www.epa.gov/ogwdw000/lt2/training/module_basicmicroscopy/scopage_dir/basic/basic.html

http://micro.magnet.fsu.edu/primer/java/dic/dicphaseos/index.html

http://www.invitrogen.com/site/us/en/home/References/Molecular-Probes-The-Handbook.html

1.0 Introduction1.0 Introduction

Environment?Environment? Microbiology?Microbiology?

Chemistry?Chemistry?

EnvironmentEnvironmentMicrobiologyMicrobiologyChemistryChemistry

Are these subjects linked at all?

Let’s take one step at a time & ask Let’s take one step at a time & ask ourselves what comes to our mind ourselves what comes to our mind

when we talk about when we talk about EnvironmentEnvironment, , MicrobiologyMicrobiology &&

Chemistry?Chemistry?

pressure

Abiotic

Biosphere

Pollution

Atmosphere

Hydro~

Litho~

Natural

Man-made

Biochemical

Physico-chemical

Biodegradation WeatheringC-H-O-N-P-S-metal cycles

Biogeochemical

Metabolism

Electron acceptors

Energy source

Radiation

pH

temperature

GasH2O

Carbon source

Radiation

Organic

In-organic

In-organic

O2

Fe(III)

NO3

SO4

Predator

Competitor

Symbiosis

Parasitism

Plate count

Most probable number (MPN)

Genetic

Polymerase Chain Reaction (PCR)Phylochip

Biochemical

ATPPhospholipids

Commensalism

Mutualism

Stoichiometry

Chemical reactions

Analytical methods

Precipitation

Redox

Acid-base

Spectroscopy

Chromatography

Spectrophotometry

Atomic Absorption Spectroscopy

Mass Spectroscopy

X-Ray

Voltammetry

Gas Chromatography

HPLC

Mole

Molar Mass

Chemical equations

Biotic

Growth Growth conditionsconditions

PhysiologyEcology

Detection

MicrobiologyChemistry Environment

As you can see it’s quite a lot!! As you can see it’s quite a lot!! How can we make sense of all How can we make sense of all these topics and illustrate their these topics and illustrate their

relationships??relationships??

Mind maps may be the solution…Mind maps may be the solution…

Example of a mind map to increase understanding and perspectives by asking questions.

What is Happiness? A personal exploration of the subject by Paul Foreman

An overview of the key "laws" of Mind Mapping, all of which aim to maximise the usefulness of the technique.

Principles of Mind Maps

Example of a mind map to increase understanding and perspectives by asking questions.

Let’s play a Let’s play a GAMEGAME and prepare to and prepare to built our own mind-map!built our own mind-map!

1.1. How does it work?How does it work?Form 5 teams A to E (draw cards provided);Form 5 teams A to E (draw cards provided);Rules: Rules: Teams take turn to pick keyword and assign to Teams take turn to pick keyword and assign to correct category (Environment, Microbiology, correct category (Environment, Microbiology, Chemistry).Chemistry).Individual team member must take turns to select Individual team member must take turns to select and assign correct category.and assign correct category.For each correct assignment team will receive one For each correct assignment team will receive one point.point.If team cannot answer correctly within 90 sec other If team cannot answer correctly within 90 sec other teams have chance to answer and earn the point.teams have chance to answer and earn the point.Team with maximum points will be CHAMPION.Team with maximum points will be CHAMPION.

pressure

Abiotic

Biosphere

Pollution

Atmosphere

Hydro~

Litho~

Natural

Man-made

Biochemical

Physico-chemical

Biodegradation WeatheringC-H-O-N-P-S-metal cycles

Biogeochemical

Metabolism

Electron acceptors

Energy source

Radiation

pH

temperature

GasH2O

Carbon source

Radiation

Organic

In-organic

In-organic

O2

Fe(III)

NO3

SO4

Predator

Competitor

Symbiosis

Parasitism

Plate count

Most probable number (MPN)

GeneticPolymerase Chain Reaction (PCR)

Phylochip

Biochemical

ATPPhospholipids

Commensalism

Mutualism

Stoichiometry

Chemical reactions

Analytical methods

Precipitation

Redox

Acid-base

SpectroscopyChromatography

Spectrophotometry

Atomic Absorption Spectroscopy

Mass Spectroscopy

X-Ray

Voltammetry

Gas Chromatography

HPLC

Mole

Molar Mass

Chemical equations

Biotic

Growth Growth conditionsconditions

PhysiologyEcology

Detection

MicrobiologyChemistry Environment

Q1: Which of the following “sphere” statements is correct?Q1: Which of the following “sphere” statements is correct?

A - Biosphere is part of the atmosphere.A - Biosphere is part of the atmosphere.

B – Atmosphere, biosphere and hydrosphere are B – Atmosphere, biosphere and hydrosphere are part of the lithospherepart of the lithosphere

C – Biosphere is part of the environment and C – Biosphere is part of the environment and comprises of atmosphere, hydrosphere and comprises of atmosphere, hydrosphere and lithosphere.lithosphere.

D – All of the above.D – All of the above.

Q2: TRUE or FALSE?Q2: TRUE or FALSE?

A – Physico-chemical weathering of A – Physico-chemical weathering of rocks / minerals is caused by micro-rocks / minerals is caused by micro-organisms and their metabolic by-organisms and their metabolic by-products.products.

B – Physico-chemical weathering of B – Physico-chemical weathering of rocks / minerals is caused by i) water rocks / minerals is caused by i) water undergoing repeated cycles of freezing & undergoing repeated cycles of freezing & thawing, ii) extreme temperature thawing, ii) extreme temperature fluctuations between day and night time, fluctuations between day and night time, and iii) acid rain dissolving minerals.and iii) acid rain dissolving minerals.

C – Biochemical processes in the C – Biochemical processes in the environment involve the breakdown of environment involve the breakdown of organic and inorganic compounds organic and inorganic compounds through microbial action.through microbial action.

Q3: How can we best describe abiotic factors?Q3: How can we best describe abiotic factors?

A) The non-living components of the environment, A) The non-living components of the environment, such as air, rocks, soil, water, peat, and plant litter.such as air, rocks, soil, water, peat, and plant litter.

B) Non-living chemical and physical factors in the B) Non-living chemical and physical factors in the environment such as radiation, temperature, pH, environment such as radiation, temperature, pH, pressure and water.pressure and water.

C) Abiotic factors are part of a special category of C) Abiotic factors are part of a special category of food additives designed to improve the nutritional food additives designed to improve the nutritional value of food.value of food.

D) It is a mathematical term referring to algebra of D) It is a mathematical term referring to algebra of bounded operators on a Hilbert space that is closed bounded operators on a Hilbert space that is closed in the weak non-living operator.in the weak non-living operator.

Q4: Stoichiometry in chemistry is defined as the relation Q4: Stoichiometry in chemistry is defined as the relation between the quantities of substances that take part in between the quantities of substances that take part in a reaction. Which of the following stoichiometric a reaction. Which of the following stoichiometric equations are correct?equations are correct?

A) CHA) CH44 (g) + O (g) + O22 (g) → 2CO (g) → 2CO22 (g) + H (g) + H22O (g)O (g)

B) 2OB) 2O22 (g) + CH (g) + CH44 (g) → CO (g) → CO22 (g) + 2H (g) + 2H22O (g)O (g)

C) 2KOH (aq) + Fe(NOC) 2KOH (aq) + Fe(NO33))33 (aq) → Fe(OH) (aq) → Fe(OH)33 (s) + 2KNO (s) + 2KNO3 3 (aq)(aq)

D) NaOH + HD) NaOH + H22SOSO44 → Na → Na22SOSO44 + 2H + 2H22O (aq).O (aq).

Q5: What is the correct definition and unit for molarity?Q5: What is the correct definition and unit for molarity?

A) Mass of solute per number of A) Mass of solute per number of moles moles of solution (e.g. mg/mol).of solution (e.g. mg/mol).

B) Number of moles of solute per B) Number of moles of solute per mass mass of solvent (e.g. mol / kg).of solvent (e.g. mol / kg).

C) Number of moles of solute per C) Number of moles of solute per volume of solution (e.g. volume of solution (e.g.

kmol dmkmol dm-3-3).).

D) None of the above.D) None of the above.

Correct Answers!Correct Answers!

1 c1 c 1 Mark1 Mark2 a : False2 a : False 1 Mark1 Mark2 b : Correct2 b : Correct 1 Mark1 Mark2 c : Correct2 c : Correct 1 Mark1 Mark3 b3 b 1 Mark1 Mark4 b4 b 1 Mark1 Mark5 c5 c 1 Mark1 Mark

7 Marks7 Marks

Let’s built our own mind-map!Let’s built our own mind-map!

1. Write the title in centre of piece of paper.1. Write the title in centre of piece of paper. Try and use keywords if possible. Try and use keywords if possible.

2. As a first level branch create a “Chemistry” 2. As a first level branch create a “Chemistry” branch. Then under this create following sub-branch. Then under this create following sub- branches: Kinetics, Equilibrium, Analytic, branches: Kinetics, Equilibrium, Analytic, Reactions, Stoichiometry Reactions, Stoichiometry

3. For the rest of your mind map add 13. For the rest of your mind map add 1stst level level branches for each of the main topics of this branches for each of the main topics of this subjects. subjects.

pressure

Abiotic

Biosphere

Pollution

Atmosphere

Hydro~

Litho~

Natural

Man-made

Biochemical

Physico-chemical

Biodegradation WeatheringC-H-O-N-P-S-metal cycles

Biogeochemical

Metabolism

Electron acceptors

Energy source

Radiation

pH

temperature

GasH2O

Carbon source

Radiation

Organic

In-organic

In-organic

O2

Fe(III)

NO3

SO4

Predator

Competitor

Symbiosis

Parasitism

Plate count

Most probable number (MPN)

GeneticPolymerase Chain Reaction (PCR)

Phylochip

Biochemical

ATPPhospholipids

Commensalism

Mutualism

Stoichiometry

Chemical reactions

Analytical methods

Precipitation

Redox

Acid-base

SpectroscopyChromatography

Spectrophotometry

Atomic Absorption Spectroscopy

Mass Spectroscopy

X-Ray

Voltammetry

Gas Chromatography

HPLC

Mole

Molar Mass

Chemical equations

Biotic

Growth Growth conditionsconditions

PhysiologyEcology

Detection

MicrobiologyChemistry Environment

CHEMISTRYCHEMISTRYENVIRONMENTENVIRONMENT

Processes

Biotic Factors

Growth Growth conditionsconditions Microscope

Epi-fluorescence

Light ~

Chemical Equilibrium

Kinetics

Order

Second

Zero

First

Acid Base

HA H+ + A-

pAbiotic Factors

Biosphere

Pollution

Atmo~

Hydro~

Litho~

Natural

Man-madeBiochemical

Physico-chemical

Biodegradation WeatheringC-H-O-N-P-S-metal cycles

Biogeochemical

Metabolism

Electron acceptors

Energy source

Radiation

pH

T

GasH2O

Carbon source

Radiation

Organic

In-organic

In-organic

O2 Fe(III) NO3 SO4

Predator

Competitor

Symbiosis

Parasitism

Plate count

MPN

GeneticPCR

PhylochipBiochemical

ATPPhospho-

lipids

Commensalism

Mutualism

Stoichiometry

Chemical reactions

Analytical

Precipitation

Redox

Acid-base

Spectroscopy

Chromatography

SpectrophotometryAAS

MS

X-Ray

Voltammetry

GC HPLC

Mole Molar Mass

Chemical equations

Experiment 1:Experiment 1:

“Chemical Redox Reaction”“Chemical Redox Reaction”

TASKSTASKS(refer to electronic handout)(refer to electronic handout)

1. Read the provided CoSHH / RA forms carefully and sign if you understand and agree with 1. Read the provided CoSHH / RA forms carefully and sign if you understand and agree with the content.the content.2. Prepare a 100 g aqueous solution containing 100 mg Cr(VI) / kg and 10 % w/w H2. Prepare a 100 g aqueous solution containing 100 mg Cr(VI) / kg and 10 % w/w H22SOSO44..

3. In increments, add premeasured amount of 1 M FeSO3. In increments, add premeasured amount of 1 M FeSO44 (or 1 M Na (or 1 M Na22SOSO33), whatever ), whatever

provided by personnel) to 100 g aqueous acidified solution (task 2) and monitor Cr(VI) provided by personnel) to 100 g aqueous acidified solution (task 2) and monitor Cr(VI) concentration based on the 1,5 diphenylcarbohydrazide method. Notice any change in concentration based on the 1,5 diphenylcarbohydrazide method. Notice any change in colour and appearance.colour and appearance.4. Define mol, molarity and molality.4. Define mol, molarity and molality.5. Calculate the molarity and molality of Cr in the aqueous solution (from 5. Calculate the molarity and molality of Cr in the aqueous solution (from task 2task 2).).6. Define ‘6. Define ‘redox-reactionredox-reaction’ and determine which reactant (Cr(VI), FeSO’ and determine which reactant (Cr(VI), FeSO44) is the oxidizing and ) is the oxidizing and

reducing agent.reducing agent.7. Establish the stoichiometric equation for the redox reaction based on the half-reaction 7. Establish the stoichiometric equation for the redox reaction based on the half-reaction method.method.8. Plot the normalized Cr(VI) concentration (C8. Plot the normalized Cr(VI) concentration (Ccr[vi]cr[vi] / C / Ccr[initial]cr[initial]) vs. molar ratio X (n) vs. molar ratio X (nFeFe / n / nCr[VI]Cr[VI]) and ) and

apply suitable trendline (linear, polynomial, exponential).apply suitable trendline (linear, polynomial, exponential).9. Compare theoretical stoichiometric equation (9. Compare theoretical stoichiometric equation (task 7task 7) with experimental values. Discuss ) with experimental values. Discuss potential causes if discrepancies between theoretical and experimental values are observed potential causes if discrepancies between theoretical and experimental values are observed (>10 % difference).(>10 % difference).10. Describe the principle of the 1,5 diphenylcarbohydrazide method and identify to which 10. Describe the principle of the 1,5 diphenylcarbohydrazide method and identify to which category of analytical method it belongs to.category of analytical method it belongs to.

Submit your lab report in 2 weeks time (counting starts from day of lab experiment).Submit your lab report in 2 weeks time (counting starts from day of lab experiment).

LAB RULESLAB RULES

1. LABORATORY SAFETY REGULATION1. LABORATORY SAFETY REGULATION2. CHEMICAL HANDLING2. CHEMICAL HANDLING3. PERSONAL SAFETY & PERSONAL RESPONSIBILITY3. PERSONAL SAFETY & PERSONAL RESPONSIBILITY4. HOUSEKEEPING4. HOUSEKEEPING5. WASTE DISPOSAL5. WASTE DISPOSAL6. PERSONAL PROTECTION EQUIPMENT6. PERSONAL PROTECTION EQUIPMENT7. LABORATORY SAFETY EQUIPMENT7. LABORATORY SAFETY EQUIPMENT8. LABORATORY’S EQUIPMENT SAFETY8. LABORATORY’S EQUIPMENT SAFETY9. FIRST AID AND EMERGENCY PROCEDURES9. FIRST AID AND EMERGENCY PROCEDURES10. FIRE ACTION PLAN10. FIRE ACTION PLAN

LAB INDUCTION SEMINARLAB INDUCTION SEMINAR

When?When? : Tuesday, 1-2PM: Tuesday, 1-2PMWhere?Where? : DK1: DK1