cee 210 environmental biology for engineers lecture: microbial groups instructor: l.r. chevalier...

CEE 210 ENVIRONMENTAL BIOLOGY FOR ENGINEERS

Lecture: Microbial Groups

Instructor: L.R. ChevalierDepartment of Civil and Environmental EngineeringSouthern Illinois University Carbondale

Environmental Biology

for Engineers

ObjectivesReview basic classifications of

microorganismsUnderstand the importance of

microorganisms to engineered systems Identify organisms important to these

systemsCalculate theoretical oxygen demand for

aerobic degradation Review the main concept of denitrification


for Engineers

Importance of MicroorganismsEfficient and cost-effective means of treating

municipal sewageCritical to the recovery processes of natural

environments degraded by human activities◦ Self-purification of streams receiving sewage and

runoff◦ Natural attenuation of industrial contaminants leaked

or spilled onto soil Create environmental problems

◦ Deplete oxygen◦ Generate unpleasant tastes and odors◦ Clog equipment◦ Corrode pipes◦ Produce disease in humans, other animals and plants


for Engineers

Key Evolutionary Steps for Microbial LifeTime Frame (billion years before present)

Duration (billion years)

Geological and Biological Activity

Geologic Time (%)

~ 4.6-3.9 0.7 Earth formed; no life; chemical evolution

~15

Origin of life; anaerobic environment

Oxygen production by cyanobacteria; emergence of aerobic bacterial life

Shift to aerobic atmosphere; emergence of more complex eukaryotic cells

Development of more advanced life


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Discovery of Microbial Life

First to use magnifying lens for the study of microbial life

Bacteria, protozoan, algae and fungi


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Louis Pasteur 1822-1895

Pasteurization of wineMicrobial metabolism


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Ferdinand Cohen (1828 –1898)

Established the field of bacteriology.

His classification of bacteria into four groups based on shape (sphericals, short rods, threads, and spirals) is still used today.


for Engineers

Heinrich Herman Robert Koch (1843-1910)

German physician Isolated Bacillus

anthracis (1877), the Isolated Tuberculosis

bacillus (1882) Isolated Vibrio cholera

(1883) Awarded the Nobel Prize

in Physiology or Medicine for his tuberculosis findings in 1905.

He is considered one of the founders of microbiology


for Engineers

_____________ In 1892, Russian scientist Dimitri Ivanowsky showed

that tobacco mosaic disease was caused by an agent smaller than any known bacteria.

In 1898, Dutch scientist Martinus Beijerinck realized that the agent was distinct from bacteria and termed it a virus.

The same year (1898), the German scientists Friedrich Loeffler (1852-1915) and Paul Frosch, both former students and assistants of Robert Koch (1843-1910), observed that a similar agent was responsible for foot-and-mouth disease. In spite of these findings, there was resistance to the idea that these mysterious agents might have anything to do with human diseases.


for Engineers

Energy Source

Energy


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Carbon Source

Energy

Chemotrophs:Chemical Oxidation

OrganotrophsOrganic

LithotrophsInorganic

Phototrophs:Photosynthesis

Carbon

fungi

protozoa

most bacteria

algae

some bacteria


for Engineers

Metabolism

Metabolism is the term for a series of chemical reactions that provide energy in a form the organism can use for its own purposes: repairing cells, excreting wastes, making new cells, and reproducing.

In over-simplified terms, the energy comes from an electron that is donated at the beginning of the process and accepted by another atom at the end of the process.

Anaerobic metabolism uses a variety electron acceptors, but not oxygen. Aerobic metabolism uses oxygen as the electron acceptor.


for Engineers

Environmental Conditions: Oxygen

____________•Require oxygen•Molecular oxygen is the terminal electron

acceptor•Microaeorphilic (very low oxygen)

_____________•Do not require oxygen•Obligates cannot grow in presence of O2

•Facultative can grow with or without O2

•Inorganic terminal electron acceptor include nitrates, nitrite, ferric iron, sulfate, CO2

______________•In environmental engineering , oxygen is

absent but nitrate and/or nitrite are present


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Environmental Conditions: Temperature

_________•Cold temperature•0° C to mid-teens•Polar ocean waters

__________•Moderate temperatures•Vast majority of microbial life

___________•45°-50°C•Bacteria, archaea, and fungi

___________•80°C or higher


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Extreme Temperature:

Mammoth Hot Springs, Yellowstone National Park, Wyoming


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Extreme Temperature

Hot spring vent at Mammoth Hot Springs, Yellowstone National Park. Maximum vent temperature is approximately 74 degrees. Photo by Jack Farmer Aarchaebacterial

streamers from near the hot spring vent in the previous image. The streamers coat all surfaces of the vent. Photo by Jack Farmer.

Microscopic view of archaebacterial filaments that form the streamers shown in the previous image. The filaments become mineralized and preserved as the spring cools. Image by Jack Farmer.

http://www.bact.wisc.edu/Bact303/b14


for Engineers

Extreme Temperature: Additional Facts of Interest The “world record”; for life growing at high temperatures is

_____ Enzymes from thermophiles are useful commercially

◦ Enzymes are added to many washing detergents because they can “eat away” the oily stains on clothing in hot water

Enzymes are also useful in genetic research◦ Thermophilic DNA enzyme Taq polymerase is used to make copies

of DNA pieces◦ First obtained from the thermophile Thermus aquaticus from

Yellowstone National Park◦ This thermophile creates the yellow-mustard color found in many

hot springs around Yellowstone’s Lower Geyser Basin Biotechnology companies have also been selling similar

enzymes from deep-sea hydrothermal vent thermophiles. ◦ Enzymes are called Pfu polymerase and have helped us to discover

genetic diseases, find criminals who may have left hair or blood at the crime scene and sequence the entire human genome


for Engineers

This shows a cross-section view of a thermophile. Notice all the viruses in the cell. Viruses are much smaller than bacteria and are abundant at deep-sea vents. Photograph: Terry Beveridge

Thermophiles may assist in creating terraced rock structures like these, located at Mammoth Hot Springs, Yellowstone National Park, USA. Astrobiologists are interested in how these rocks because it gives them insights into how rocks may form on other planets.

These stringy thermophiles make sulfur and with time they harden and fossilize into rock.

Billions of thermophiles clump together and create this yellow-mustard color at Mushroom Hot Spring in Yellowstone National Park.

Extreme Temperature: Additional Facts of Interest


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Environmental Conditions: Salinity

Microbial cells have different ionic strength (salt) within cytoplasm than outside

Water migrates across the cell membrane toward the higher salt zone by osmosis

Microbial cells resist this fluid movement, and the harm excessive shrinking and swelling can cause, to a certain degree

_________ microbes are salt loving◦ Seawater is 3% NaCl◦ These microbes requires concentrations above 15%


for Engineers

Environmental Conditions: Salinity

Cells of Halobacterium as seen through a high-powered microscope. The individual cells in this image are about 5 microns long.

The Dead Sea is 5+ times saltier than Earth's oceans. As water evaporates, salt is left behind. When the saturation point is reached, the salt forms these pillars. Credit: Purdue University.


for Engineers

More on this amazing bacteria Researchers at the University of Maryland have

exposed the bacteria to numerous harsh environmental conditions ◦ Radiation◦ Extreme dryness◦ Vacuum of space

Bacteria survive!◦ DNA repaired

Future research◦ Biotechnology frontier◦ Scientist have found Halobacterium encased in salt

deposits 250 million years old (this claim is controversial) May lead to discoveries of life on other planets, such as

Mars, where water has evaporated


for Engineers

Environmental Conditions: pH

_____________◦ pH 5-9

_____________◦ pH 1-2◦ Acid mine drainage water◦ Acidic hot spring waters

_____________◦ pH > 9◦ Dead Sea◦ Soils high in carbonates

Electron micrograph of Natronococcus occultus. This extremely halophilic and alkaliphilic spherical shaped organism was isolated by H.N.M.Ross from Lake Magadi, Kenya.


for Engineers

Uses of Extreme Bacteria

The bacterium Shewanella oneidensis strain MR-1 (above) may offer a biological solution for remediating US sites contaminated during the manufacture of nuclear weapons.

Deinococcus radiodurans thrives in radiation levels thousands of times higher than those that would kill most organisms, including humans, and it may prove useful in bioremediation of toxic waste.


for Engineers

Theoretical Oxygen DemandWe have tools that allow us to predict the

amount of oxygen needed for aerobic organisms to break down waste

The theoretical oxygen demand is just that,….theoretical. Bacterial decomposition is not necessarily 100% efficient◦ Mixed waste◦ Mixed bacterial populations◦ Temperature, pH, salinity◦ Rates of decomposition◦ Also have chemical oxidation


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Theoretical Oxygen DemandProcedure

◦ Determine the chemical formula for the waste◦ Balance the following equation

C_H_O_ + _O2 _CO2 + _H2O

For example, consider glucose, C6H12O6

C6H12O6 + 6O2 6CO2 + 6H2O


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Theoretical Oxygen DemandProcedure

C6H12O6 + 6O2 6CO2 + 6H2O

◦ This balanced equation can be read in two ways One molecule of glucose requires 6 molecules of

oxygen One mole of glucose requires 6 moles of oxygen

◦ Convert moles to grams For glucose, the MW is 6(12) +12(1) + 6(16) = 180

g/mole Since there is only one mole of glucose, we can say

that it takes 192 grams of oxygen to oxidize 180 grams of glucose


for Engineers

Theoretical Oxygen DemandWhat if nitrogen is present

◦ Glycine C2H5O2N (MW 75 g/mole)

In the first step, the glycine will be converted to◦ Carbon dioxide, CO2

◦ Ammonia, NH3

In a subsequent step, the bacteria will break down the nitrogen

The theoretical oxygen demand in this case will be the sum of the oxygen used both steps


for Engineers

Theoretical Oxygen DemandGlycine C2H5O2N (MW 75 g/mole)Balance equation

◦ C_H_O_N_ + _O2 _NH3 + _CO2+_H2O

◦ Compare this to the equation without nitrogen C_H_O_ + _O2 _CO2 + _H2O

From this equation, we now consider the decomposition of ammonia to nitric acid ◦ _NH3 + _O2 _HNO3 +_ H2O

Nitric acid is commonly used in fertilizers and explosives

Microbial denitrification can reduce this to environmentally benign N gas◦ Bacteria, fungi, simple eukaryotes


for Engineers

Theoretical Oxygen Demand


for Engineers

DenitrificationDenitrifying bacteria include

◦ Pseudomonas thiobacillus◦ Micrococcus denitrificans

The natural cycle of denitrification involves a stepwise reduction of nitrate to nitrogen◦ NO-

3 NO-2 NO N2ON2

Consider the following example of microbial denitrification◦ In the absence of oxygen but with carbohydrates

present, microbes obtain energy by denitrification

◦ C6H12O6 + 4NO-3 6CO2 + 6H2O + 2N2

Thiobacillus


for Engineers

ObjectivesReview basic classifications of

microorganismsUnderstand the importance of

microorganisms to engineered systems Identify organisms important to these

systemsCalculate theoretical oxygen demand for

aerobic degradation Review the main concept of denitrification


for Engineers

ReferencesChapter 10: Microbial GroupsVirology

◦ http://www.nlv.ch/Virologytutorials/definition.htmCultivating Bacteria's Taste for Toxic Waste

by Liza Gross◦ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC15267

65/

BioEd Online◦ http://www.bioedonline.org/◦ Lecture slides on:

Introduction to Biological Classification Introduction to Organisms Introduction to Viruses

http://www.nlv.ch/Virologytutorials/definition.htm

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526765/


http://www.bioedonline.org/


for Engineers

Images Antoni van Leeuwenhoek, Louis Pasteur, Robert Koch

◦ Wikimedia Commons

Dimitri Ivanowsky, Martinus Beijerinck, Friedrich Loeffler◦ Virology

◦ http://www.nlv.ch/Virologytutorials/definition.htm

Mammoth Hot Springs, Yellowstone National Park, Wyoming ◦ Photo by Larry Fellows http://www.earthscienceworld.org

Some like it hot◦ http://www.astrobio.net/exclusive/80/some-like-it-hot

Halobacterium and Dead Sea ◦ Secrets of a Salty Survivor

http://science.nasa.gov/headlines/y2004/10sep_radmicrobe.htm

Image ofNatronococcus occultus◦ http://www.dsmz.de/dsmz/main.php?content_id=17

Image of Shewanella oneidensis Deinococcus radiodurans ◦ Cultivating Bacteria's Taste for Toxic Waste by Liza Gross


◦ US Department of Energy Office of Science http://genomicscience.energy.gov/science/microbialfunction.shtml

Image of Thiobacillus ◦ Biochemical Cycles http://filebox.vt.edu/users/chagedor/biol_4684/Cycles/Soxidat.html

http://www.dsmz.de/dsmz/main.php?content_id=17

http://filebox.vt.edu/users/chagedor/biol_4684/Cycles/Soxidat.html


for Engineers

Sources of photographs and images in sidebar

Human brain

◦ http://www.healthnak.com/mind/

X-rays images

◦ http://martingallerycharleston.com/index.html

Cold Virus (altered in Photoshop)

◦ http://medphoto.wellcome.ac.uk/

About the Instructor

Professor, Civil and Environmental Engineering

Fellow, American Society of Civil Engineers (ASCE)

Diplomat, Water Resources Engineering, American Academy of Water Resources Engineering (AAWRE)

Board Certified Environmental Engineer, American Academy of Environmental Engineers (AAEE)

Licensed Professional Engineer, State of Illinois

http://www.healthnak.com/mind/

http://martingallerycharleston.com/index.html

http://medphoto.wellcome.ac.uk/

cee 210 environmental biology for engineers lecture: microbial groups instructor: l.r. chevalier...

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