Microbial Ecology E&EB 340

Meeting Information

When: TTh 9:00-10:15

Where: OML 201

Instructors 

Martina Dal Bello, PhD (she, her, hers) martina.dalbello@yale.edu

Elizabeth Blackmore elizabeth.blackmore@yale.edu

Office hours

During weekly office hours I am available to answer questions, discuss the course materials, and broadly be of support. Please drop in to attend office hours on Zoom or in person. If you have a scheduling conflict and you are not able to attend regular office hours, please email me to schedule an appointment.

When: Th 10:30-11.30

Office location: OML 327C

Zoom link: https://yale.zoom.us/j/93630473723

Course Description

When thinking about microbes what comes to mind are usually diseases and unpleasant smells from the fridge or the basement. Nevertheless, microbes and the communities they form are key contributors to our wellbeing and the functioning of the planet. This course provides an introduction to microbial ecology, with an emphasis on how microbial systems differ from their macroscopic counterparts, including defining a microbial species; sampling/experimenting with microbes; principles of microbial growth, metabolism, and death; species interactions and community assembly in different environments; microbial community functions; elements of microbial evolution.

Although the content is specific to microbial ecology, this course is designed to allow students to get a general understanding of the process of discovery in science and develop skills (such as the ability to collaborate and communicate when working in teams) that will become handy over the course of their career.

 Format

Microbial ecology is designed to incorporate both lectures and discussions: topics will be introduced in class, but a deeper understanding will be gained through discussion of the materials. All students will be expected to complete readings in advance of each session and respond to pre-class reading questions. Graduate students are expected to present a mini-lecture on a special topic in microbial ecology.

Prerequisites

BIOL 101,102, 103, & 104. General Ecology E&EB 220 and MCDB 290 are encouraged but not required.

Learning Objectives

By the end of this course, you will be able to:

  • Explain the methodological challenges associated with the study of microbes

  • Predict the effect of environmental stressor of cellular functions and population dynamics

  • Predict the outcome of microbial interactions in different environments

  • Estimate growth parameters from cell density temporal profiles

  • Process 16S rRNA amplicon sequencing data to estimate the structure of microbial communities

  • Weight bottom-up and top-down approaches to study the ecology of microbial communities

  • Justify the inclusion of microbial processes into climate change predictions

The activities proposed in E&EB 340 are designed to help you develop the following general competencies:

  • Diagnosis and design: The ability to generate questions, translate them into testable hypotheses and design appropriate experiments

  • Team-work: The ability to cover various roles in a group of peers, value and question everyone’s opinion while respecting it.

  • Communication: The ability to effectively deliver your ideas using oral, written and graphical means of communication.

Required Materials

  • Required textbook: Biology of microorganisms 16th Edition ISBN 9780134874401 (Michael T. Madigan, Kelly S. Bender, Daniel H. Buckley, W. Matthew Sattley, David A. Stahl, Pearson Education)

  • Additional readings will be drawn from the primary literature and Life’s engines (Paul G. Falkowski, Princeton University Press) ~14$ on Amazon

 Please take a look at the Tentative schedule for a class-by-class list of readings.

Assessments & Grading

Grading breakdown for undergraduate students

Class preparedness and participation 15%
Assignments 15%
Mid-term exam 25%
Final exam (not comprehensive) 25%
Final paper 20%

Class preparedness and participation (15%)

Students are expected to attend classes, actively participate to in-class activities and discussions, respond to pre-class reading questions.

Assignments (15%)

Assignments, either in-class or at-home, are going to be distributed across the semester (see Tentative calendar for details). The grade reflects on-time submission, meeting the word-count requirements/or providing the right solution in case of problem sets, and clarity in the communication. Examples of assignments include: prompts for questions, written summaries of papers from the primary literature, and data analyses exercises. Assignments’ due dates will be highlighted on canvas and announced in class. All assignments must be submitted through canvas and not via email.

Mid-term and final exams (50% total)

The midterm and final exams are meant as summative assessment of the material covered in class and the assigned readings. Both are held in class, closed-books.

Final paper (20%)

Students will be writing mini review paper in the Current Opinion in Microbiology style. The mini-review should cover papers on the selected topic discussed in class, in addition to a few additional papers selected by the students. It should provide new avenues for the research topic. Undergraduate students will work in teams.

Grading breakdown for graduate students

Class preparedness and participation 5%
Assignments 15%
Mid-term exam 25%
Final exam (not comprehensive) 25%
Final paper 30%

Graduate students will work independently on the final project and will give a short presentation in class on their work. The review paper will count for 20% of the grade, while the presentation will count for 10% of the grade. 

 Please take a look at the Tentative schedule for a weekly breakdown of assignments.

Academic Integrity

In this course, I will hold you to the high standard of academic integrity expected of all students at Yale. I do this for three reasons. First, it is essential to the learning process that you are the one doing the work. Failing to do the work yourself will result in a lesser understanding of the content, and therefore a less meaningful education for you. Second, plagiarism (i.e., the use of someone else’s work, words, or ideas as if they were your own) goes at detriment of your own development: always give credit and add your own reflections! Third, violating the Academic Integrity policy in any way (e.g., plagiarism, unauthorized collaboration, cheating, etc.) results in official sanction. Possible sanctions include receiving a failing grade on the assignment or exam, being assigned a failing grade in the course, and expulsion for very serious cases.

Collaboration: Collaboration is essential for learning and doing science. I encourage you to work cooperatively on the homework assignments, although ultimately each of you is responsible for the solution/fulfillment of every homework problem set or assignment. Collaboration is not permitted during exams.

AI policy: AI chatbots can be useful learning tools if used appropriately. A good policy is to treat these resources similarly to discussions with peers or other web resources — i.e., you can consult them freely but must understand and write up your answers (including code) independently and you cannot directly copy/paste from any sources, including ChatGPT. Another good way of thinking about it is that for AI suggestions to be useful you need to have clear expectations on what should be the output of your request to a bot. In addition, you should acknowledge any use of AI to complete an assignment by citing the prompt you submitted to the bot, the date of access, and the URL of the program. Always ask the bot for references, check them thoroughly as they can be inaccurate, and report them. 

Please review the Academic Integrity policy and other resources (e.g., writing advice from the Poorvu Center for Teaching and Learning) and contact me if you have any questions about appropriate citation methods, the degree of collaboration that is permitted, or anything else related to the Academic Integrity of this course.

Diversity, Equity, Inclusion, & Belonging

This class strives to be an inclusive environment. We believe in the importance of fostering transparency, belonging, and collaboration, as there are the bases for free inquiry and growth. We welcome individuals of all backgrounds, beliefs, ethnicities, national origins, gender identities, sexual orientations, religious and political affiliations – and other visible and non-visible differences. We reject all forms of prejudice and discrimination. Everyone is encouraged to offer and be receptive to constructive criticism, express opinions while respecting someone else’s point of view, be open about accepting mistakes, pursue disagreement without aggression and handle it with care. I expect everyone to actively contribute to build a space where everyone feels respected and safe. If this standard is not being upheld, please feel free to speak with me.

Accessibility

Each of us learns differently and I am committed to developing a course that is inclusive in its design.  If there are aspects of this course that represents barriers to your learning, let me know as soon as possible. I am open to develop strategies to enable your success, as long as they do not compromise the goal of the learning activity or the assessment.  You are encouraged to contact Student Accessibility Services to find out how to improve your learning experience for this and other courses. There are also other resources, including the Writing Center, Residential College Tutors, and Academic Strategies. I welcome any suggestion to improve the learning experience for all students.

Tips

How to succeed in this course:

  • Engage thoughtfully with the course material, the readings and the assignments

  • Do not hesitate to ask for help (to me, to your peers) and provide feedback

  • Take advantage of failure

  • Think like an ecologist.