CEE 210 Environmental Biology for Engineers

1. Lecture: Microbial Groups CEE 210 Environmental Biology for Engineers Instructor: L.R. Chevalier Department of Civil and Environmental Engineering Southern Illinois University Carbondale

2. Objectives • Review basic classifications of microorganisms • Understand the importance of microorganisms to engineered systems • Identify organisms important to these systems • Calculate theoretical oxygen demand for aerobic degradation • Review the main concept of denitrification

3. Importance of Microorganisms • Efficient and cost-effective means of treating municipal sewage • Critical 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

4. Key Evolutionary Steps for Microbial Life

5. Discovery of Microbial Life First to use magnifying lens for the study of microbial life Bacteria, protozoan, algae and fungi

6. Louis Pasteur 1822-1895 Pasteurization of wine Microbial metabolism

7. 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.

8. 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

9. _____________ • In 1892, Russian scientist DimitriIvanowsky showed that tobacco mosaic disease was caused by an agent smaller than any known bacteria. • In 1898, Dutch scientist MartinusBeijerinck 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.

10. Energy Source

11. Carbon Source

12. 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.

13. Environmental Conditions: Oxygen

14. Environmental Conditions: Temperature

15. Extreme Temperature: Mammoth Hot Springs, Yellowstone National Park, Wyoming

16. Extreme Temperature Hot spring vent at Mammoth Hot Springs, Yellowstone National Park. Maximum vent temperature is approximately 74 degrees. 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. Aarchaebacterialstreamers from near the hot spring vent in the previous image. The streamers coat all surfaces of the vent. Photo by Jack Farmer.

17. 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 thermophileThermusaquaticus 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

18. Extreme Temperature: Additional Facts of Interest These stringy thermophiles make sulfur and with time they harden and fossilize into rock. 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. Billions of thermophiles clump together and create this yellow-mustard color at Mushroom Hot Spring in Yellowstone National Park.

19. 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%

20. 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.

21. 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

22. Environmental Conditions: pH Electron micrograph of Natronococcusoccultus. This extremely halophilic and alkaliphilic spherical shaped organism was isolated by H.N.M.Ross from Lake Magadi, Kenya. • _____________ • pH 5-9 • _____________ • pH 1-2 • Acid mine drainage water • Acidic hot spring waters • _____________ • pH > 9 • Dead Sea • Soils high in carbonates

23. Uses of Extreme Bacteria The bacterium Shewanellaoneidensis strain MR-1 (above) may offer a biological solution for remediating US sites contaminated during the manufacture of nuclear weapons. Deinococcusradiodurans 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.

24. Theoretical Oxygen Demand • We 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

25. Theoretical Oxygen Demand • Procedure • 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

26. Theoretical Oxygen Demand • Procedure • 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

27. Theoretical Oxygen Demand • What 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

28. Theoretical Oxygen Demand • Glycine 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

29. Theoretical Oxygen Demand

30. Denitrification • Denitrifying bacteria include • Pseudomonas thiobacillus • Micrococcus denitrificans • The natural cycle of denitrification involves a stepwise reduction of nitrate to nitrogen • NO-3 NO-2 NO N2ON2 • 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

31. Objectives • Review basic classifications of microorganisms • Understand the importance of microorganisms to engineered systems • Identify organisms important to these systems • Calculate theoretical oxygen demand for aerobic degradation • Review the main concept of denitrification

32. References • Chapter 10: Microbial Groups • Virology • http://www.nlv.ch/Virologytutorials/definition.htm • Cultivating Bacteria's Taste for Toxic Waste by Liza Gross • http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526765/ • BioEd Online • http://www.bioedonline.org/ • Lecture slides on: • Introduction to Biological Classification • Introduction to Organisms • Introduction to Viruses

33. Images • Antoni van Leeuwenhoek, Louis Pasteur, Robert Koch • Wikimedia Commons • DimitriIvanowsky, MartinusBeijerinck, 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 ofNatronococcusoccultus • http://www.dsmz.de/dsmz/main.php?content_id=17 • Image of ShewanellaoneidensisDeinococcusradiodurans • Cultivating Bacteria's Taste for Toxic Waste by Liza Gross http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526765/ • 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

34. 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