Introduction to Microbiology: Canadian Edition
Welcome to Microbiology: Canadian Edition. This textbook is an adaptation of the OpenStax textbook Microbiology. Material from the OpenStax textbook was transferred to the Pressbooks platform, maintaining much of the content of the original, with the exception of sections on the helminths. In addition to the transfer of html OpenStax files to the Pressbooks platform, this adaptation primarily involved the addition of more basic microbiology and microbial ecology, in order to broaden the target audience. Some of the original OpenStax material was updated or moved to new sections or chapters, in order to expand on certain topics. The chapter on “Microbial Ecology and Applied Microbiology” (Ch. 10) is entirely new. Additional open resources were used to supplement the new material, as summarized in the table below. In some instances, Canadian examples or stories have been added. The discussion on Microbial Ecosystem Therapeutics in Sec. 10.4 was written by Dr. Emma Allen-Vercoe, Professor and Tier 1 Canada Research Chair in the Department of Molecular and Cellular Biology, University of Guelph. She is co-founder of NuBiyota, a company established to develop “Microbial Ecosystem Therapeutics” to treat disorders resulting from gut microbial dysbiosis.
Microbiology: Canadian Edition is licensed under a Creative Commons Attribution 4.0 International License, except where otherwise noted.
OER supplementary source
|1.1||New topic: “Birth of microbiology”||N|
|2.4||FISH for ID of pathogens||N|
|3.2||Discussion of controversy on the structure of the universal Tree of Life, and the current evidence in support of a 2-domain ToL||N|
|3.3||Description of unique lipids and structure of the archaeal plasma membrane
Additional discussion on the role of the prokaryotic plasma membrane in processes associated with eukaryotic organelles
Detailed discussion of membrane transport in bacteria and archaea
|4.2||More detailed description of quorum sensing in the Hawaiian bobtail squid||Boundless Microbiology|
|4.3||Discussion of anaerobic ammonia oxidation and the anammoxasome of the Planctomycetes||Boundless Microbiology|
|4.5||Discussion of controversy of the deep-branching placement of extremophilic bacteria and the higher mutation rates in the extremophiles||N|
|4.6||More detail on the Archaea, in particular, their phylogeny||Microbiology by Linda Bruslind & Boundless|
|8.1||Added discussion of Gibbs free energy
More detailed discussion of oxidation & reduction in metabolism
|OpenStax Biology 2e
Microbiology by Linda Bruslind
|8.3||More detailed discussion of electron transport systems
More detailed discussion of anaerobic respiration
|Microbiology by Linda Bruslind|
|8.6||New section on lithotrophy||Microbiology by Linda Bruslind|
|8.7||More detail on microbial phototrophy||Microbiology by Linda Bruslind|
|9.1||New section on biosynthesis
Microbiology by Linda Bruslind
|9.2||More detail on microbial growth||N|
|9.3||More detail on media used for microbial growth”||Microbiology by Linda Bruslind|
|9.6||More discussion on the effects of temperature on growth, and the adaptations to temperature extremes and fluctuations||Microbiology by Linda Bruslind|
|9.7||More discussion on environmental osmolarity, and the adaptations to osmotic extremes and fluctuations||Microbiology by Linda Bruslind|
|10||Introduction to new chapter: “Microbial Ecology and Applied Microbiology”||Microbiology by Linda Bruslind and Boundless Microbiology|
|10.1||New section: “Microbial Ecology & Metagenomics”||Boundless Microbiology & OpenStax My Derived Biology Collection & Boundless Microbiology|
|10.2||New section: “Microbial Symbioses: Lichens and Mycorrhizae”||Boundless Microbiology|
|10.3||New section: “Methanogens & Syntrophy”||Boundless Microbiology|
|10.4||New section: “Biotechnology”||Openstax Concepts of Biology & OpenStax Biology 2e|
|10.5||New section: “Water Pollution and Bioremediation”||OpenStax Biology 2e & OpenStax Environmental Science & Boundless Microbiology|
In addition to being able to take advantage of the tremendous efforts of others and their open education publications, this University of Guelph adaptation has involved a real team effort both at the University of Guelph and beyond. At UofG, Claire Coulter, Instructional Technology Specialist at UofG’s Open Learning and Educational Support first introduced me to the idea of OER, creative commons licensing and worked hard to get this project off the ground. Ali Versluis, UofG’s Open Education Resources Librarian, has been a constant source of advice, expertise and ongoing encouragement and support. Heather Martin, Copyright Officer & Manager, E-Learning & Reserves was indispensable, providing copyright advice, in particular, with figures I needed and couldn’t find in the Creative Commons. In those cases, I designed new figures, Heather vetted them, and the final digital versions were produced through collaboration with Melanie Parlette-Stewart, Digital Media Librarian & President, Ontario College and University Library Association, as well as her very talented coop students from Ontario’s Western University Master of Library and Information Science program, Anne He and Allie Fallis. Peggie French, Program Manager of eCampus Ontario provided access to the eCampus instance of Pressbooks, and introduced me to the process of OER publication. I am very grateful to Lillian Hogendoorn, Digital Access and OER Lead at eCampusOntario: Lillian has really clarified a number of aspects of OER publication and answered various questions/solved a few problems, related to the OpenStax to Pressbooks transfer, Pressbooks idiosyncrasies and/or my own learning curve. This book has taken longer to complete than expected, but through it all, Ali Versluis and Lillian have responded to my questions and resolved technical issues right away. Finally, I could not have taken on this project without having received teaching release from my S18 teaching, when this project first began, and I thank Claire Coulter and Ali, for making the case to Rebecca Graham, University Librarian, Rebecca for providing the funding for that release, and my departmental Chair, Dr. Marc Coppolino, for his support of this project.
Microbiology: Canadian Edition is licensed under a Creative Commons Attribution 4.0 International (CC BY) license, which means that you can distribute, remix, and build upon the content, as long as you provide attribution to the author. You are free to use the entire book or pick and choose the sections that are most relevant to the needs of your course. Feel free to remix the content by assigning your students certain chapters and sections in your syllabus, in the order that you prefer. You can even provide a direct link in your syllabus to the sections in the web view of your book.
If you have corrections or suggestions regarding content (for the second edition), please e-mail the author: firstname.lastname@example.org. Any corrections will be documented in the version history in the back matter of this text.
American Society of Microbiology (ASM) Partnership
OpenStax Microbiology was produced through a collaborative publishing agreement between OpenStax and the American Society for Microbiology Press. The book was developed to align to the curriculum guidelines of the American Society for Microbiology.
The American Society for Microbiology is the largest single life science society, composed of over 47,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences.
ASM advances the microbial sciences through conferences, publications, certifications, and educational opportunities. It enhances laboratory capacity around the globe through training and resources and provides a network for scientists in academia, industry, and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences and is committed to offering open-access materials through their new journals, American Academy of Microbiology reports, and textbooks.
ASM Recommended Curriculum Guidelines for Undergraduate Microbiology Education
PART 1: Concepts and Statements
- Cells, organelles (e.g., mitochondria and chloroplasts) and all major metabolic pathways evolved from early prokaryotic cells.
- Mutations and horizontal gene transfer, with the immense variety of microenvironments, have selected for a huge diversity of microorganisms.
- Human impact on the environment influences the evolution of microorganisms (e.g., emerging diseases and the selection of antibiotic resistance).
- The traditional concept of species is not readily applicable to microbes due to asexual reproduction and the frequent occurrence of horizontal gene transfer.
- The evolutionary relatedness of organisms is best reflected in phylogenetic trees.
Cell Structure and Function
- The structure and function of microorganisms have been revealed by the use of microscopy (including bright field, phase contrast, fluorescent, and electron).
- Bacteria have unique cell structures that can be targets for antibiotics, immunity and phage infection.
- Bacteria and Archaea have specialized structures (e.g., flagella, endospores, and pili) that often confer critical capabilities.
- While microscopic eukaryotes (for example, fungi, protozoa and algae) carry out some of the same processes as bacteria, many of the cellular properties are fundamentally different.
- The replication cycles of viruses (lytic and lysogenic) differ among viruses and are determined by their unique structures and genomes.
- Bacteria and Archaea exhibit extensive, and often unique, metabolic diversity (e.g., nitrogen fixation, methane production, anoxygenic photosynthesis).
- The interactions of microorganisms among themselves and with their environment are determined by their metabolic abilities (e.g., quorum sensing, oxygen consumption, nitrogen transformations).
- The survival and growth of any microorganism in a given environment depends on its metabolic characteristics.
- The growth of microorganisms can be controlled by physical, chemical, mechanical, or biological means.
Information Flow and Genetics
- Genetic variations can impact microbial functions (e.g., in biofilm formation, pathogenicity and drug resistance).
- Although the central dogma is universal in all cells, the processes of replication, transcription, and translation differ in Bacteria, Archaea, and Eukaryotes.
- The regulation of gene expression is influenced by external and internal molecular cues and/or signals.
- The synthesis of viral genetic material and proteins is dependent on host cells.
- Cell genomes can be manipulated to alter cell function.
- Microorganisms are ubiquitous and live in diverse and dynamic ecosystems.
- Most bacteria in nature live in biofilm communities.
- Microorganisms and their environment interact with and modify each other.
- Microorganisms, cellular and viral, can interact with both human and nonhuman hosts in beneficial, neutral or detrimental ways.
Impact of Microorganisms
- Microbes are essential for life as we know it and the processes that support life (e.g., in biogeochemical cycles and plant and/or animal microbiota).
- Microorganisms provide essential models that give us fundamental knowledge about life processes.
- Humans utilize and harness microorganisms and their products.
- Because the true diversity of microbial life is largely unknown, its effects and potential benefits have not been fully explored.
PART 2: Competencies and Skills
- Ability to apply the process of sciencea. Demonstrate an ability to formulate hypotheses and design experiments based on the scientific method.b. Analyze and interpret results from a variety of microbiological methods and apply these methods to analogous situations.
29. Ability to use quantitative reasoning
a. Use mathematical reasoning and graphing skills to solve problems in microbiology.
30. Ability to communicate and collaborate with other disciplines
a. Effectively communicate fundamental concepts of microbiology in written and oral format.
b. Identify credible scientific sources and interpret and evaluate the information therein.
31. Ability to understand the relationship between science and society
a. Identify and discuss ethical issues in microbiology.
Microbiology Laboratory Skills
- Properly prepare and view specimens for examination using microscopy (bright field and, if possible, phase contrast).
- Use pure culture and selective techniques to enrich for and isolate microorganisms.
- Use appropriate methods to identify microorganisms (media-based, molecular and serological).
- Estimate the number of microorganisms in a sample (using, for example, direct count, viable plate count, and spectrophotometric methods).
- Use appropriate microbiological and molecular lab equipment and methods.
- Practice safe microbiology, using appropriate protective and emergency procedures.
- Document and report on experimental protocols, results and conclusions.
Microbiology: Canadian Edition Correlation to ASM Recommended Curriculum Guidelines for Undergraduate Microbiology Education
|OpenStax Microbiology Correlation to ASM Curriculum Guidelines|
|Chapter||ASM Curriculum Guidelines|
|1—An Invisible World||2, 4, 5, 11, 16, 20, 23, 26, 27, 31|
|2—How We See the Invisible World||6, 31, 32, 33|
|3—The Cell||1, 2, 5, 9, 16, 21, 25, 31|
|4—Prokaryotic Diversity||2, 4, 8 ,11, 12, 16, 20, 23, 24, 31|
|5—The Eukaryotes of Microbiology||2, 4, 5, 9, 12, 20, 23, 31|
|6—Acellular Pathogens||4, 10, 18, 23, 31|
|7—Microbial Biochemistry||1, 24, 33, 34|
|8—Microbial Metabolism||1, 11, 12, 13, 22, 24|
|9—Microbial Growth||12, 13, 29, 31, 33, 34, 35|
|10—Microbial Ecology and Applied Microbiology
11—Biochemistry of the Genome
|11, 12, 14, 20, 22, 23, 24, 26, 27, 31
1, 16, 25, 31
|12—Mechanisms of Microbial Genetics||1, 2, 15, 16, 17, 31|
|13—Modern Applications of Microbial Genetics||19, 26, 31|
|14—Control of Microbial Growth||13, 14, 26, 31, 36, 37|
|15—Antimicrobial Drugs||3, 7, 14, 15, 23, 26, 31|
|16—Microbial Mechanisms of Pathogenicity||8, 9, 10, 15, 18, 23, 33|
|17—Disease and Epidemiology||7, 14, 23, 26, 31|
|18—Innate Nonspecific Host Defenses||7, 8, 23|
|19—Adaptive Specific Host Defenses||7, 23, 26, 31|
|20—Diseases of the Immune System||7, 8, 24|
|21—Laboratory Analysis of the Immune Response||31, 34|
|22—Skin and Eye Infections||8, 9, 10, 14, 18, 23, 24, 31|
|23—Respiratory System Infections||7, 8, 9, 14, 18, 23, 24, 31|
|24—Urogenital System Infections||7, 8, 9, 12, 14, 18, 22, 23, 24, 31|
|25—Digestive System Infections||7, 8, 9, 10, 14, 18, 23, 24, 31|
|26—Circulatory and Lymphatic System Infections||7, 8, 9, 14, 23, 31|
|27—Nervous System Infections||7, 8, 9, 14, 18, 23, 24, 31|
Engaging Feature Boxes
Throughout Microbiology: Canadian Edition, feature boxes have been maintained from the original OpenStax book. These features were designed to engage students by taking selected topics a step further. They include:
- Clinical Focus. With the exception of the entirely new Chapter (10), each chapter has a multi-part clinical case study that follows the story of a fictional patient. The case unfolds in several realistic episodes placed strategically throughout the chapter, each episode revealing new symptoms and clues about possible causes and diagnoses. The details of the case are directly related to the topics presented in the chapter, encouraging students to apply what they are learning to real-life scenarios. The final episode presents a Resolution that reveals the outcome of the case and unpacks the broader lessons to be learned.
- Case in Point. In addition to the Clinical Focus, many chapters also have one or more single-part case studies that serve to highlight the clinical relevance of a particular topic. These narratives are strategically placed directly after the topic of emphasis and generally conclude with a set of questions that challenge the reader to think critically about the case.
- Micro Connections. All chapters contain several Micro Connections feature boxes that highlight real-world applications of microbiology, drawing often-overlooked connections between microbiology and a wide range of other disciplines. While many of these connections involve medicine and healthcare, they also venture into domains such as environmental science, genetic engineering, and emerging technologies. Moreover, many Micro Connections boxes are related to current or recent events, further emphasizing the intersections between microbiology and everyday life.
- Sigma Xi Eye on Ethics. This unique feature, which appears in most chapters, explores an ethical issue related to chapter content. Developed in cooperation with the scientific research society Sigma Xi, each Eye on Ethics box presents students with a challenging ethical dilemma that arises at the intersection of science and healthcare. Often grounded in historical or current events, these short essays discuss multiple sides of an issue, posing questions that challenge the reader to contemplate the ethical principles that govern professionals in healthcare and the sciences.
- Disease Profile. This feature, which is exclusive to Chapters 22–27, highlights important connections between related diseases. Each box also includes a table cataloguing unique aspects of each disease, such as the causative agent, symptoms, portal of entry, mode of transmission, and treatment. These concise tables serve as a useful reference that students can use as a study aid.
- Link to Learning. This feature provides a brief introduction and a link to an online resource that students may use to further explore a topic presented in the chapter. Links typically lead to a website, interactive activity, or animation that students can investigate on their own.
Materials That Reinforce Key Concepts
- Learning Objectives. Every section begins with a set of clear and concise learning objectives that are closely aligned to the content and Review Questions.
- Key Takeaways. The Key Takeaways text box, at the end of each section, distills the information from that section into a series of concise bullet points.
- Key Terms. With the introduction of each new term, a definition follows. Definitions of key terms are also listed in the Glossary in (Appendix E).
- Check Your Understanding questions. Each subsection of the text is punctuated by one or more comprehension-level questions. These questions encourage readers to make sure they understand what they have read before moving on to the next topic.
- Review Questions. Each chapter has a robust set of review questions that assesses students’ mastery of the Learning Objectives. Questions are organized by format: multiple choice, matching, true/false, fill-in-the-blank, short answer, and critical thinking.
About the Author
Wendy Keenleyside, University of Guelph
Dr. Wendy Keenleyside received her BSc in Microbiology and Immunology from the University of Western Ontario, her MSc in Microbiology from the University of Toronto, and her PhD in Microbiology from the University of Guelph. Her graduate training was in the area of bacterial pathogenesis, with her PhD and post-doctoral research focused on the genetics and physiology of E. coli and Salmonella cell surface polysaccharide expression. She has been teaching at UofG since 1994, and has been a full-time Instructor-Coordinator in the in the department of Molecular and Cellular Biology since 2000, teaching courses at the 2nd-4th year levels, in microbiology, bacterial genetics, bacterial adaptation, and microbial ecology, as well as 1st year biology. After redeveloping and teaching a 4th year microbial ecology course in 2008, she became a microbial ecology convert and “evangelist”. Her teaching approach is centred on using an active learning approach and student teams, as a means of developing independent learners, creativity and critical thinking, as well as communication and team skills. She is a member of the American Society for Microbiology, the Canadian Society of Microbiologists, and the Open Consortium of Undergraduate Biology Educators (https://sites.google.com/site/ocubeorg/ ).
A list of contributors for the OpenStax edition can be found here: https://cnx.org/contents/5CvTdmJL@7.1:ryt9cF1D@13/Preface
Figure 9.16 (Sec. 9.2) – live staining and fluoresence microscopy. Viable cells are stained green, whereas dead cells are stained red. [Credit: modification of work by Panseri S, Cunha C, D’Alessandro T, Sandri M, Giavaresi G, Maracci M, Hung CT, Tampieri A]