General Overview & Introduction
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Biology 447 Environmental Microbiology Website: http://wvlc.uwaterloo.ca/biology447/ © 2011 Colin I. Mayfield Biology 447 – Environmental Microbiology Table of Contents . Biology 447: General Overview & Introduction .............................................................3 . Assignments: Introduction ........................................................................................... 11 . Background Information on Water Issues for Biology 447 ........................................ 15 . Module 1: Aquatic Microbiology ................................................................................... 21 . Biofilms ........................................................................................................................... 41 . Other Issues in Water Pollution and Microbiology ..................................................... 52 . Lake Erie - Progress and Regression ......................................................................... 64 . Module Two - Marine Microbiology ............................................................................. 67 . Module Three - Estuarine Microbiology ....................................................................... 75 . Module Four - Pathogens in Water .............................................................................. 79 . The E. coli outbreak at Walkerton, Ontario .................................................................. 90 . Module Five - Biodegradation Microbiology .............................................................. 101 . Module Six - Deep Subsurface Microbiology ........................................................... 169 . Module Seven - Groundwater Microbiology .............................................................. 172 . Module Eight - Bioremediation ................................................................................... 205 2 Biology 447 – Environmental Microbiology Biology 447: General Overview & Introduction What are the goals of the course? The course is not designed to be an intensive study of all aspects of water microbiology, but, instead, water microbiology in all of its variety is used as an example of the range of microbiological topics that directly affect environmental issues. There is an apparent concentration on groundwater and contaminated soil issues involving microbiology simply because they are less well presented in textbooks from a microbiological viewpoint. There is also a deliberate attempt in most parts of the course to put the microbiology in a context that involves other issues in the environment. These include the role of the regulating agencies, the role of the law and government agencies in setting and enforcing standards, and the assessment and reporting procedures commonly used in environmental assessment, monitoring and compliance. The assignments for the course are designed to help with this last process. You will also find that there is an evolution in the course material from the more theoretical in freshwater and marine microbiology through more applied materials in biodegradation and groundwater microbiology to very practical and applied materials in the bioremediation sections of the course. You should find, nevertheless, that many of the concepts and examples in earlier parts of the course can still be applied to the section on bioremediation. Main goals for this course: To achieve a basic understanding of aquatic microbiology and microbial processes To know the major microorganisms of importance in freshwater, seawater, and groundwater To understand the major microbial processes involved in those habitats To understand the major environmental factors and influences in those habitats To understand how to apply basic microbiological and ecological principles in understanding the applied processes known as bioremediation of contaminated soils and groundwater. Specifically: Freshwater microbiology To be able to explain the activities of microorganisms in freshwater habitats, their importance and their interactions with the environment and other organisms. To be able to assess the role and importance of freshwater habitats in disease transmission by pathogenic microorganisms and protozoa. To assess and explain the concepts of productivity, growth, biomass, diversity in freshwater habitats (including estuarine habitats) and the concept of ecosystem control measures. To have a basic understanding of the methods used in aquatic microbiology and their advantages and deficiencies To be able to judge and explain the importance, relevance and future development of microbiological and other standards and regulations. Marine microbiology To understand the differences between the marine and freshwater habitat and their influences on microbial activities. To understand the specific roles of pressure, temperature and salinity. To understand the role of undersea volcanic vents in marine microbial productivity. 3 Biology 447 – Environmental Microbiology Biodegradation To understand the role and importance of chemical structure of molecules and the effects of environmental factors on biodegradation by microorganisms. To understand the roles of these factors on the specific examples of naturally occurring compounds such as cellulose, lignin, proteins, etc., various hydrocarbons and pesticides. Groundwater microbiology To understand the roles of microorganisms in groundwater ecosystems, especially in terms of their effects on the evolution of the geochemistry and biochemical properties of groundwater systems. To relate the microbiology of groundwater to the observed changes in naturally occurring compounds introduced into groundwater. Bioremediation To be familiar with the basic principles of bioremediation activities as they are used in contaminated soil and groundwater. To be able to devise appropriate generalized systems to perform bioremediation in contaminated systems (lectures and assignments). To apply information gained from this course and reference materials in the course and from other sources to critically evaluate bioremediation processes and applications. What should I be able to accomplish by the end of the course? The course deals with aspects of water microbiology from a general point of view and uses specific examples to illustrate the concepts. For instance, details of pathogenic bacteria in freshwater are not given, but, instead, an overview of their importance, the regulations surrounding their monitoring, the methods used to detect them, and their occurrence in some habitats is studied. The intention is that this serves as an example with reference sources supplied so that you can discover other aspects of pathogenic microorganisms in water systems. For instance, water treatment technologies are not presented in detail, but references to information on water treatment is given. This approach is used for the other areas of the course. You should have the following abilities and knowledge at the end of the course: 1. Theoretical knowledge of aspects of water microbiology 2. Practical applications of knowledge base to particular problems 3. How to find, assess and integrate data and information on environmental issues 4. How to produce a report on knowledge gained that presents the information effectively 5. How to integrate knowledge from different parts of the course How to use study materials most effectively 1. The complete lecture notes for each of the modules are given on the WWW site for the sake of providing more up-to-date material than could be provided in printed lecture notes. 2. The extra material on each Module is reference material and supplementary material; it is designed to clarify and/or complement the lectures and is NOT necessarily required knowledge. Many of the external links to other sites are dependent upon them remaining active and up-to-date; many may change or even vanish very quickly. 3. The assignments can be performed most effectively using searches and the WWW pages as starting points. 4 Biology 447 – Environmental Microbiology 4. There is a tremendous amount of material on the WWW site. One of the aims of the course is to organize the material in a comprehensible manner. Another is for you to learn techniques of organization of complex materials and to be able to find, extract, categorize, organize and assess such diverse information sources. You will find that some of them are even contradictory and certainly present different views of the same topic. One of the primary goals of the last assignment is related to that problem; to allow you to learn how to produce a good, organized and comprehensive report on a topic in bioremediation based on all available information. 5. You are NOT expected to know and be able to reproduce all of the material on this WWW site. A preliminary estimate I have done indicates that there is about 2.0 gigabytes of information directly referenced on the WWW site. If you go further into each WWW site referenced, that volume could exceed 5 Gigabytes. 6. Most of the information is background or material for the assignments. Use the search functions (local and the WWW search engines) as much as you can to narrow down information to that of use to you. No-one can possibly cope with 10 Gigabytes of information at once. To put it in perspective, a typical typed page is 1 kilobyte. One thousand kilobytes (pages) is a megabyte. A thousand megabytes is a Gigabyte. Five Gigabytes is 5 million pages! A little bit more than your average textbook!! 7. Try and use the lecture material