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11:680:492: Microbial Ecology and Diversity Lab


Course Overview

Microbial Ecology and Diversity Lab

Class time:TBD
Food Science Lab 201 & Lipman Hall 325

Contact Information

Lecturer: Dr. Karla Esquilín-Lebrón;
Office (Student) Hours: Available upon request (in person or virtual meetings). Office hours are a time for all students in this class to have an opportunity to meet with me. Email me to find the best available time for us to meet.

Course Website, Resources, and Materials

  • Canvas

Course Description

Microbial Ecology and Diversity Laboratory is a 3-credit laboratory course that meets once, weekly, for 5hrs 40min (lunch break 30-45min). The lab offers students the experience to perform in-depth analyses of a microbial community from local ecosystems. Students in this course will build upon the basic principles and skills gained in introductory and mid-level courses. Laboratory exercises focus on microbial functions in ecosystems, examining the interactions between microbial communities and their environments and the impact of these relationships on biogeochemical cycles. The course explores ecological principles as they apply to microorganisms, while emphasizing the molecular, biochemical and evolutionary diversity in the microbial world.
This laboratory course is offered alternating spring semesters and is intended for upper-level undergraduate students in microbiology, biochemistry, biotechnology, environmental sciences, oceanography, and graduate students in the biosciences.

Course Learning Goals

Students will explore how the environment shapes microbial communities and how microbes affect the environment. Upon completion of the course, students will have acquired the basic skill set for participation in contemporary microbial ecology research and employment in related industries and organizations. Students will be capable of investigating microbial interactions using a multifaceted approach including culture-independent & culture-dependent analyses, bioinformatics, analytical methods, phylogeny, and ecosystem ecology. Through this course, students will develop analytical skills by applying the scientific method; including hypotheses and goals settings, experimental design, collection and analyses of data, and synthesis of data to form conclusions. This skillset includes the ability to:

  1. Communicate how environmental conditions drive community structure and assess metabolic capabilities of microbial communities.
  2. Follow the scientific method to develop and test hypothesis.
  3. Analyze and communicate scientific data from research articles (journal clubs) and the findings from experiments perform during class (research proposal & poster presentation).
  4. Develop an NSF-GRFP style research proposal aligned to one of the modules and supported by literature research.
  5. Analyze community structure data to form conclusions related to microbial interactions with each other and with their environment.
  6. Apply hands-on bioinformatics analysis of data (sequencing data and genome mining for natural product producers).

Assignments/Responsibilities, Grading, and Assessment

Research Proposal, Presentation and Peer Review (40%)
Students will use the guidelines described by the NSF-GRFP to write their research proposals based on preliminary data collected from one of the class experiments/modules. The research proposal should be prepared in a way to provide the reviewers (instructor, TA and peers) that your research plan is eligible for fellowship. The research proposal should follow the structure:

  1. Introduction: introduce the research idea, what are its broader impacts?
  2. Research plan for minimum 2 aims, each aim should contain objective/hypothesis, research approach and expected outcome.
  3. Broader impacts
  4. Conclusion
  5. Citations

Journal Club Paper and Presentation (20%)

Students will choose one seminal and one recent scientific article (within the last 5 years) related to their research project that they conduct in the lab. Students will present the papers to the class in a journal club format. A written document will accompany the presentation. Paper selection will be done in consultation with instructor. The submitted paper and presentation/discussion should include:

  1. A concise summary of the work being discussed
  2. A critical evaluation of the research
  3. An explanation of how the paper relates to the class module

Students will also be expected to participate in the discussion of other research articles during journal club. To facilitate this activity, students will prepare one question about each paper ahead of lab and submit on Canvas. Question submissions count towards 5% of the class participation grade). Students will submit a reflection after each Journal Club presentation.

Assignments, Poster Presentation, Excursions (25%)
Points will vary based on the assignments. Assignments are due before class time (Wednesday at 8:30AM) or date listed (by 11:59PM). Group excursions are incorporated throughout the course, participation is mandatory. Take detailed notes on visits and excursions. Short reports addressing a questionnaire will be submitted approximately one week following each excursion.

In-class Activities and Class Participation (5%)
Students are expected to participate in group discussions which will occur regularly throughout the semester. Throughout the semester, readings and assignments will be administered in preparation for the upcoming labs and in review of previously covered material. Activities will be submitted periodically for grading during class.

Course Policies

This syllabus contains the policies and expectations that have been established for this course. These policies and expectations are intended to create a productive learning atmosphere for all students. Please bring any concerns you may have to my attention.

Absence Policy
Class attendance is mandatory. Make-up classes are not possible. Students are expected to attend every in-person lab meeting and scheduled excursions. Assignments missed as a result of an unexcused absence will result in loss of points. Absences may only be excused if prior notification is given, and appropriate documentation provided.

Email Policy
Please use CANVAS or Scarletmail for any communications in this course. I will respond to email within 24 hours, Monday through Friday between 9am to 6pm. I reserve the right to wait until Monday to reply to messages sent over the weekend.


Oh No! Life happens clause/ Late submission
Assignments turned in late will earn 75% of points. Late submissions will only be accepted a week after the due date. No late submissions will be accepted for the research proposal project and group poster project.


Standard Semester Grades

Students are graded at the end of each course, in accordance with the grades and symbols authorized by the University Faculty Senate, as follows:

A= Outstanding (90-100)
B+ (85-89)
B=Good (80-84)
C+ (75-79)
C=Satisfactory (70-74)
D=Poor (60-69)
F=Failing (0-59)
W=ASSIGNED BY REGISTRAR to students who officially withdraw from a course


Tentative Schedule


Lab #

Module 1


Module 2

Aerobic Denitrifiers

Module 3


Module 3


Jan 18



Gradients/Interfaces Intro


Write experimental set-up

Aerobic Denitrifiers Intro


Science article search

Patch on master plates


Experiment overview


Jan 25



Winogradsky column prep (4-8 wks. For full development)


*Journal club discussion


Write experimental set-up

Bioprospecting Intro


Patch on ESKAPE relatives


++Assign journal club for Bioprospecting


Feb 1


Record observations

Enrichment/Inoculation for Aerobic denitrifying bacteria

Review patch plates

Gram stain

Metabolic tests


*Journal club discussion


Feb 8


Record observations

Culture transfers


Dilution plating for T0


Record metabolic tests


Plates for organic extraction

Methanogenesis Intro


++Assign journal club for Methanogenesis

Feb 15


Record observations

Culture transfers,

QSP to isolate


Organic extraction (day1)

*Journal club discussion


Experiment design


Feb 22


Record observations

Culture transfers, pick colonies from QSP,

Dilution plating, slants,

Metabolic test plan



Organic extraction (day2) test organic extracts




Record observations

Inoculate metabolic tests media

Gram stain



Review plates

Data analysis

Design figures

COOK Barn trip (9:30AM)

AM: Visit Hyacinth, collect rumen sample, wet mounts


PM: Experimental set-up

March /8


Record observations


++Assign JC for gradients and interfaces

Record metabolic test results


DNA extractions

PCR, product extraction


Submit samples for sequencing

Measure gas production




Spring break




                                           Cheesequake State Park Trip

                                          (Class meets at the Park @9:30AM)




Record observations

*Journal club discussion


in silico NP discovery (AntiSMASH activity)




Record observations



Data analysis

Bioinformatics and discussion

Sequencing results

Analysis of sequencing data

BLAST sequences

Phylogenetic tree




Group Winogradsky discussion

Sequencing results                                          analysis                                                    Bioinformatics and discussion



April /19


Proposal Presentations

Elevator speech competition

April /26


Career Day: CV/Resume workshop, Career Panel

Poster presentation practice



Biochemistry and Microbiology Department Symposium

Poster presentations


Academic Integrity

Read the university's policy on Academic Integrity . The principles of academic integrity require that a student:

  • properly acknowledge and cite all use of the ideas, results, or words of others.
  • properly acknowledge all contributors to a given piece of work.
  • make sure that all work submitted as his or her own in a course or other academic activity is produced without the aid of impermissible materials or impermissible collaboration.
  • obtain all data or results by ethical means and report them accurately without suppressing any results inconsistent with his or her interpretation or conclusions.
  • treat all other students in an ethical manner, respecting their integrity and right to pursue their educational goals without interference. This requires that a student neither facilitate academic dishonesty by others nor obstruct their academic progress.
  • uphold the canons of the ethical or professional code of the profession for which he or she is preparing.

Adherence to these principles is necessary in order to ensure that:

  • everyone is given proper credit for his or her ideas, words, results, and other scholarly accomplishments.
  • all student work is fairly evaluated and no student has an inappropriate advantage over others.
  • the academic and ethical development of all students is fostered.
  • the reputation of the University for integrity in its teaching, research, and scholarship is maintained and enhanced.

Failure to uphold these principles of academic integrity threatens both the reputation of the University and the value of the degrees awarded to its students. Every member of the University community therefore bears a responsibility for ensuring that the highest standards of academic integrity are upheld.

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