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Biology 355 - Microbial Ecology

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Spring 2024 Syllabus

MWF 1:00 PM – 1:50 PM (309 Hudson Hall)      


Dr. José de Ondarza, Hudson Hall 211, 564-5156


Office Hours

·         MWF 10:00 - 11:00 AM

·         By appointment



·         Barton & Northup. Microbial Ecology, 2011, Wiley Blackwell Publishers. ISBN 978-0-470-04817-7


Additional Materials

·         Weekly reading assignments will be posted online


Course Website

The course web site ( and Brightspace are the formal and official means of delivering content for Biology 355 (Microbial ecology). Students are encouraged to make use of the course-related resources (e.g. lecture notes, detailed instructions for assignments, bonus points) found on these sites.


Reading Assignments

Chapters and/or page numbers assigned for each class period are indicated on the course lecture calendar. Readings should be completed before the corresponding class period. The reading assignments are intended to illustrate, support, supplement, and expand on the class discussions. All exam questions will come from material covered in the class discussion and the assigned readings. The textbook will provide valuable examples and serve as a reference for the many terms and concepts we will cover. Many concepts are illustrated in diagrams and photos and will give you a different perspective on the content. Primary literature assigned for in-class discussion must be read before class and will form the basis for our case studies and concept review. Please take the reading assignments seriously.


Student Learning Outcomes

On completion of this course, students will be able to:

  1. Describe, and distinguish among, the different types of microbial interactions with other organisms
  2. Understand and explain the nature and significance of microbial cycling of carbon and minerals in ecosystems
  3. Discuss the importance of microbial processes in waste water treatment, industry, bioremediation and other applied disciplines
  4. Describe the structure of diverse microbial communities, including plant and animal microbiomes, biofilms, and microbiomes of unique environmental niches.        


Attendance policy

Attendance during class periods is necessary. Class discussions will cover the topics outlined in the course calendar (see below) and may contain material not covered by the textbook. Students are responsible for all material covered in class, as well as any announcements made during the class period. We will discuss new topics, apply these in practical terms, and lay the foundation for discussion of primary literature each week.



Honor Code

It is expected that all students enrolled in this class support the letter and the spirit of the Academic Honesty Policy as stated in the college catalog.


Grading policy

Your course grade will be based on the following (500 points total):

·         3 in-class exams (100 points each)

·         1 term paper (100 points)

·         Weekly quizzes (100 points)

Exams will cover material as indicated on the calendar.  Exams will consist of a mixture of short-answer, multiple choice and other questions.


Exam Corrections may be done for multiple choice sections of exams.  Exam corrections give you the opportunity to regain up to 50% of the points lost on the multiple choice section.  Corrections must be turned in within 1 week of the exam's return in class.


Term Paper: 10 pages (3000 words minimum), based on your research about a topic in Microbial ecology.   Term papers are intended to go beyond the scope of the textbook, include research into the current scientific literature, and promote your written and oral communication skills. Plagiarizing part or entirety of your paper may result in a grade of “0” for the term paper and/or the course.  Due date: May 6, 2024.


Quizzes: Weekly quizzes will be handed out/posted on Brightspace. Only the highest 10 scores will count toward your grade. 10 points each, due Mondays in class.


Extra Credit Policy: You can earn up to 15 bonus points for the semester by participating in the weekly on-line assignment (15 points). On-line assignments are posted weekly on Brightspace, are based on the special readings found on Brightspace, and cannot be made up.


Grading scale








93% – 100%


80% - 82%


67% – 69%


90% – 92%


77% – 79%


60% – 66%


87% – 89%


73% – 76%


< 60%


83% – 86%


70% – 72%




Email is the official and formal mode of communication for Bio 355, whether sent through Brightspace or the faculty email account. Emails will be sent to the email address associated with your student account.



You will be asked to read and acknowledge the course plagiarism policy found on the course Brightspace site. (Course Resources: Academic Dishonesty/Plagiarism Policy)


How will Plagiarism/Academic dishonesty be dealt with?

 Depending on the perceived severity of the offense (Intentional or inadvertent? How much of the course grade was affected? How much of an assignment was plagiarized? Was this a repeat offense?) the instructor may mark down the assignment by one letter grade, give a grade of "0" for the assignment, give a grade of "E" for the course, and/or refer the student to the campus judicial committee for academic dishonesty. This will result in a hearing before the judicial committee and may result in expulsion from the University. 


Use of electronic devices in class

All electronic devices such as computers, phones, Blackberries, iPods etc should be turned off during class time except if needed for emergency contacts. No electronic devices are permitted to be in use during exams, including but not limited to cell phones, Blackberries, iPods, calculators, and electronic dictionaries. If you require special testing conditions, please contact Student Support Services.


Writing Standards for Department of Biological Sciences

 It is the position of the Department of Biological Sciences at Plattsburgh State that all students must learn to write in a clear and intelligent manner.  We recognize that this goal cannot be achieved by depending only on the efforts of others to foster good writing. We further believe that the general quality of student writing will not improve unless we as a department are willing to state explicitly the standards we expect students to meet and to enforce those standards.  Therefore, in courses taught by the Department of Biological Sciences, in addition to grading the content of written assignments, all faculty will also grade assignments for writing.


Course help will be available to you in various ways. Please feel free to come to my office during office hours to discuss course-related questions or problems. If you cannot make it in during regular office hours, please schedule an alternate time with me. Many questions can also be addressed via email, and I encourage you to use this approach. I will attempt to answer each message I receive within a day.

Student Accommodations
SUNY Plattsburgh is committed to providing reasonable accommodations for all persons with disabilities. If you are a student with a disability that may have an impact on your work in this class and require academic or other accommodations, please contact the Accessibility Resources Office (ARO) on the first floor of Feinberg Library 127, call 518-564-3844 or email You may also Request Accommodations from the Accommodate portal and a representative will contact you directly. To utilize specific accommodations you must certify with this office prior to accommodations being provided.


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