PPEM 297: Special Topics (Fall 2017, Section From the Tame to the Wild: the Environments and Ecologies of Microbes)

Formal courses given infrequently to explore, in depth, a comparatively narrow subject which may be topical or of special interest.


  • Plant Pathology and Environmental Microbiology


Welcome to introductory microbial ecology and environmental microbiology. By participating in PPEM 297 From the Tame to the Wild: the Environments and Ecologies of Microbes, students will develop an understanding of both the abiotic and biotic contexts in which microbes thrive, as well as how humans have taken advantage of microbial processes, particularly in agricultural settings. This course will draw on the diverse fields of microbiology, ecology, evolution, physiology, genetics, and geochemistry, among others. Thus, there are many questions that microbial ecologists and environmental microbiologists can ask and many methods by which they can go about forming an answer.

Course Logistics

Instructor: Dr. Kevin L. Hockett, Assistant Professor, Department of Plant Pathology and Environmental Microbiology
Office: 316 Buckhout Laboratory
Phone: 814-865-4472
Office Hours: Tues/Thurs | 1:30-2:30 p.m. or by appointment

Class Meeting Times: Tuesdays/Thursdays | 12:05-1:20 p.m.
Class Location: 103 Buckhout Laboratory
Grading: Letter, 3 credit hours
Prerequisites: BIOL 110/110H or BIOL 011 or MICRB 106
Canvas Course Site

Course Objectives

By the end of this course, students should be knowledgeable regarding the fundamentals and applications of microbial ecology and environmental microbiology.

The course is separated into four main sections:

  • fundamental concepts
  • technologies and tools
  • microbes in wild environments
  • microbes in managed environments

In fundamental concepts we will cover key figures and ideas surrounding the development of microbial ecology and environmental microbiology (lecture 1). We will then move on to familiarizing ourselves with the major groups of microbes, followed by discussing critical aspects of a microbe’s biology that determines the sorts of environments it will be able to inhabit (lectures 2-4). We will wrap up this section by looking at microbial-host interactions (lecture 5) and microbe-microbe interactions (lecture 6).

In technologies and tools we will focus on contemporary and traditional tools used in microbial ecology, including omics technologies as applied to two basic questions: “Who’s there?” and “What're they doing?” (lectures 7-8).

In microbes in wild environments we will look at the general and specific factors that influence the presence of microbes across distinct environments as well as how microbes help shape these environments (lectures 11-17). We will conclude this section by looking at the critical roles of microbes in cycling key nutrients (lectures 19 and 21).

To wrap up the lecture portion of the class with microbes in managed environments, we will examine the ways in which humans have influenced and taken advantage of microbial-driven processes for our benefit, particularly within agricultural settings (lectures 22-31).


Although there is no required text for this course, reading material will be posted from Microbial Ecology by Barton and Northrup (Wiley-Blackwell), Environmental Microbiology: From Genomes to Biogeochemistry by Eugene Madsen (Wiley Blackwell). This text will be supplemented with review articles, materials from other books, and primary research articles, all of which will be available to students through the Canvas course website.


Students are expected to attend lectures to gain the most from this course. Lecture slides will be posted to Canvas typically the evening before the lecture is given, however, this is not guaranteed.


Grades will be determined by the following components:

ComponentTotal Pts% Final Grade
Weekly quizzes 150 15
Exam I 200 20
Exam II 200 20
Exam III 200 20
Term project 250 25
Extra credit 50* 5*
TOTAL 1050 100

Weekly quizzes will be given at the beginning of the Tuesday lecture each week and will focus on the material covered the previous two periods (previous week). Answers to each quiz will be discussed immediately following the Quiz. Quizzes will consist of 3 to 5 questions (including a combination of multiple choice, true/false, fill in the blank, and short answer questions). The two lowest quiz scores for each student will be dropped, including missed quizzes due to a student's absence.

Exams will consist of approximately equal portions of short answer (1-2 sentences), short essay (1-2 paragraphs), and multiple choice questions. Mock questions and answers will be provided to students two days prior to the exam.

Term project. Each student will choose one from the following two options:

    1. Proposal-based inquiry (5-10 double-spaced pages): In this project, students will both identify a current question as it pertains to microbial ecology and propose research to be conducted that will address that question. This project is split roughly evenly between research into the particular question and research into the application of experimental protocols and techniques.
    2. Review-based inquiry (5-10 double-spaced pages): In this project, students will review an aspect of current microbiological literature from an ecological or environmental perspective. This project differs from the proposal-based inquiry in that it does not require a proposal of research to be conducted (and thus will require less focus on specific techniques), but will require more integration of a current question into an ecological or environmental (or both) context.

Details concerning specific requirements, timelines, and guidelines for evaluation for each of the term projects will be provided by the fourth week of class (Sept. 12 and 14 lecture week).

Extra credit will be available for students to earn points (up to 5 percent of the final grade) by writing potential exam questions. Specific instructions regarding extra credit will be given in the second week.


Students are expected to attend class regularly with motivation to engage and learn the course material. Students are equally expected to dedicate time outside of lecture to read and review course material, as this is required for mastery of the subject. As a rule of thumb, students should be spending at least 2-3 hours studying course material for every hour of lecture.

Equally, the instructor is expected to be prepared and organized for each lecture, to furnish resources required to understand the material (e.g., readings, slides, and other material that is appropriate), to be reasonably available outside of class to assist student learning in areas where they have difficulties, and to help guide students through a successful and satisfying term project.

Course Resources

Reading requirements will be paired with each lecture. The course readings will be available for download from the Canvas course website. These reading assignments are intended to reinforce and supplement lecture material. It is recommended that students read the material for a particular lecture prior to the lecture, as this will help students gain the most from lectures.

How to Succeed in this Class

This class is a mix of ecological, environmental and microbiological concepts, technologies, and factors. As such, it will be advantageous for students to be comfortable in linking specific ideas to general concepts. Additionally, as the class proceeds, material will build on previous material. For example, when discussing plant- or animal-associated microbes, students will need to recall technologies and concepts described previously. This means that it is critical for students to learn the course material as it is being taught, and if a particular idea or concept is unclear, students should seek to remedy the situation in a timely manner (i.e., see me during office hours to discuss problematic material the same week that the material is introduced). Learning is an active process, thus students that actively engage the material will do well in this class.

Methods that helped me learn material as a student that may help you include: a) teaching the material to a fellow classmate (nothing will point out gaps in your understanding better than attempting to teach it to a fellow student) and b) writing up lecture material to produce an outline of the important points and examples presented in each lecture, as well as how the reading material relates to the lecture material.

Science is often opaque to people largely because of its jargon (specialized terms with specific meaning). This means that you, as students, need to ensure that you understand how to correctly use the jargon presented in this class, as well as the underlying concepts behind this jargon. Nothing will make your understanding (or lack thereof) of the subject material more clear than your use (or misuse) of jargon.

Course Schedule

Aug 22 1 Introduction, History of Microbial Ecology and Environmental Microbiology
Aug 24 2 Microbial Diversity
Aug 29 3 Microbial Physiology and Metabolism
Aug 31 4 Microbial Growth
Sept 5 5 Symbioses with Hosts
Sept 7 6 Population Interactions: from Biofilms to Syntrophy
Technologies and Tools
Sept 12 7 Who's There: Methods to Identify Microbes
Sept 14 8 What're They Doing: Methods to Assess Microbial Functions
Microbes in Wild Environments
Sept 19 9 Biogeography: Dispersal, Environments, and Communities
Sept 21 10 Exam I
Sept 26 11 Plant-Associated Microbes
Sept 28 12 Soil-Associated Microbes
Oct 3 13 Animal-Associated Microbes
Oct 5 14 Aquatic Environments
Oct 10 15 Bacteriophage-Bacteria Interactions in Marine Environments
Oct 12 16 Atmospheric Microbes
Oct 17 17 Extreme Environments
Oct 19 18 Guest Lecture: Terrence Bell, Ph.D.
Oct 24 19 Decomposition
Oct 26 20 Exam II
Oct 31 21 Biogeochemical Cycling
Microbes in Managed Environments
Nov 2 22 Guest Lecture: Prem Kandel, Ph.D.
Nov 7 23 Sewage Treatment
Nov 9 24 Plant Growth Promotion via Symbioses
Nov 14 25 Biocontrol and Suppressive Soils
Nov 16 26 Movement and Detection of Pathogens in Agricultural Settings
Nov 21 27 Thanksgiving Holiday - No Class
Nov 23 28 Thanksgiving Holiday - No Class
Nov 28 29 Microbial Source Tracking
Nov 30 30 Clostridium difficile and Antibiotic Treatment in Humans
Dec 5 31 Bioremediation of Xenobiotics
Dec 7 32 Exam III

**Schedule and topics will be subject to change as needed. Students will be informed of schedule changes in advance when possible.

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