BIOLOGY 335*            LIMNOLOGY AND AQUATIC ECOLOGY (Fall 2016)           

|Course Information| |Lecture Schedule and links to PDF Files| |Labs, Fieldtrip & Assignments| |Brian's website|

Welcome to the Biology 335 (Limnology) website. The main goal of this site is to give information on this course, links to PDF files of the lectures, PDFs of the labs, as well as PDFs of some essential papers.  Please use the userid and password given to you in class to access the PDF files. 


Professor:       Brian F. Cumming

Professor, Biology/School of Environmental Studies

Head, Department of Biology; Co-director, Paleoecological Environmental Assessment and Research Lab (PEARL).
Offices:  Room 3102, Bioscience Complex (Main Office), Room 4307b (PEARL, office).
Contact Information:  533-6153 (phone); e-mail:

Teaching Assistants (TAs):

----Liz Favot---- ----Cecilia Barouillet---Cale Gushulak--Clare Nelligan

e-mails:;; Cale Gushulak (; Clare Nelligan (

Limnology is a large subject that considers geological, physical and chemical aspects of inland waters, as well as their biology and development.  Obviously, in a half course we cannot attempt to consider all facets of limnology in depth.  We attempt to present an overview, emphasizing fundamental interactions and processes.  The objectives of the course are to provide you with a basic understanding of the physical, chemical, and biological processes in lakes, as well as an appreciation of the impact of human activities on these waterbodies.

Course material will be presented by three approaches ‑ in formal lectures, laboratories, and a compulsory one-day (either Saturday, October 1, or Sunday, October 2) field trip to the Queen's University Biology Station (QUBS) on Lake Opinicon. There is overlap between these approaches, but they are not redundant and require integration.

There is a strong practical component to this course beginning with the field trip when you will receive a crash course in limnological surveys.  You will receive an introduction to many facets of limnological methodology including chemical and biological sampling techniques, and plankton identification.  In only a few of these aspects will you receive any further practice or amplification in later laboratory periods.  From the data you collect on the field trip and additional information you will be given, you will be expected to answer questions on the exams.   

If you have any questions or concerns about the course, please feel free to contact me or your DSC (to be selected by your class). It is best to try to talk to me immediately following the lectures. However, if this is not possible, my e-mail is, and my main office (Rm. 3102) in the Biosciences Complex (the phone number for both offices is 533-6153).

Lectures: Tuesday (12:30-1:20), Thursday (11:30 -12:20) and Friday (13:30 - 14:20), Jeffery Hall, Rm. 225.

Labs:  Every other week (total 5 labs) + one-day compulsory fieldtrip (Saturday, Oct. 1 or Sunday, Oct. 2) [Three Sections:Tuesday, 8:30-11:30 am (capacity: 26 students); Wednesday, 2:30 - 5:30 pm (capacity, 13 students); Friday, 2:30-5:30 pm (capacity 26 students).

Please show upto your lab time in the first week of classes -- your demonstrators will go over important organizational and safety information.

Lab times: All labs are held in Rm. 3320 of the Bioscience Complex.

Fieldtrip:   In this course we have a compulsary one-day fieldtrip to the Queen's University Biology Station (QUBS) (Saturday Oct. 1, or Sunday Oct. 2). We will leave at 7:30 sharp, and will return by approximately 6 pm the same day. The cost of the fieldtrip will be $30. Please bring either a cheque or cash to your first lab. This cost will cover the cost of transportation to and from the Biology Field Station, user fees, and lunch.

Required Textbook: Wetzel, R. G. 2001.  Limnology: Lake and River Ecosystems (3nd edition), Academic Press (available at the Campus Book Store). 

Marking Scheme:
A) Assignment 1:  Lake Models (Lab 1) - 10%;
B) Midterm exam - 20% - covers material upto the end of the Physical and Chemical Limnology section of this course
C) Assignment 2:  Paleoecology (Lab 4) - 15%;
D) Lab exam - 15%;
E) Final exam - 40% -  held during the normal exam period.  The focus of the final exam will be on material covered in the latter part of the course. Examination questions may also include material covered in labs and the field day.


Generally, I will try to get the PDF files up onto the website 24 to 48 hrs prior to the lecture.

PLEASE NOTE: These notes represent most of the visuals shown in the lectures. They do not represent all of the information you will require, as much more is discussed in the lectures than appears on these visuals. PLEASE take notes in class, it is an important skill you have to develop in university.


  Lecture Topic Date (day) Chapter Lecture Title
Week 1 Introduction                  Sept. 13 (Tu, 12:30)      1                     



    Lab Introduction (all groups, ~ 1hr)   Show up to your scheduled lab

Physical Limnology     

Sept. 15 (Th, 11:30) 2, 4, 5             

Water Properties and Light 


Sept. 16 (F, 1:30) 


Heat and Lake Stratification

Week 2   Sept. 20 (Tu, 12:30) PDF Lewis Lake Classification
    Lab 1, Group 1 PDF Vallentyne Lab 1 (Group A) - Lake Models
    Sept. 22 (Th, 11:30) 7 Water Movements
    Sept. 23 (F, 1:30)   3                       Origin of Lakes
Week 3 Chemical Limnology

Sept. 27 (Tu, 12:30)  

9                    Oxygen
    Lab 1, Group 2   Lab 1 (Group B)- Lake Models

Sept. 29 (Th, 11:30) 

10 Salinity I
    Sept. 30 (F, 1:30)  

Salintiy II + Intro to Field trip (included in PDF above)

  Opinicon Fieldtrip Oct 1(Sat) or Oct. 2 (Sun): 7:30 am to 6 pm.   Field manual (please read before field day)
Week 4   Oct 4 (Tu, 12:30)                              
11 Inorganic Carbon
    Lab 2, Group 1    
  Lab 2 (Group A) –Chemical Limnology; Assignment 1 due for Group A (Lab 1)
    Oct 6 (Th, 11:30)  
12                    Nitrogen Cycle
    Oct. 7 (F, 1:30)       13; also see paper: Camareo & Catalan, Nature (2012)   Phosphorus Cycle
Week 5   Oct 11 (Tu, 12:30)   Micronutrients (S, Si)
    Lab 2, Group 2   Lab 2 (Group B) –Chemical Limnology; Assignment 1 due Group B (Lab 1)
    Oct. 13 (Th., 11:30)      

Case Study - Lake Nyos

  No class Oct. 14 (F, 1:30)                                
Week 6   Oct. 18 (Tu, 12:30) Example midterm

MIDTERM (in class)

    Lab 3, Group 1 Lab 3 (Group A) – Phytoplankton and Zooplankton

Primary/ Secondary Production

Oct. 20 (Th, 11:30)      

Intro. to Algae

Oct. 21 (F, 1:30)

15                    Ecology of Algae
Week 7  

Oct. 25 (Tu, 12:30)     

15                    Seasonality
    Lab 3, Group 2   Lab 3 (Group B) – Phytoplankton and Zooplankton

Oct. 27 (Th, 11:30)    

16                    Zooplankton (ZP)
    Oct. 28 (F, 1:30)                     
16 Fish and Trophic Interactions
Week 8 Integrative Limnology   Nov. 1 (Tu, 12:30)      
24                   Introduction to Paleolimnology
    Lab 4, Group 1                  
  Lab 4 (Group A) – Paleolimnology
    Nov 3 (Th, 11:30)                               Lake Acidification

Nov 4 (F, 1:30)                               

  Applied Paleolimnology-Acidification in the Adirondacks
Week 9  

Nov. 8 (Tu, 12:30)                             

  Multiple stressors in the Adirondacks
    Lab 4, Group 2    Lab 4 (Group B) – Paleolimnology

Nov. 10 (Th, 11:30)                        

Cumming et al. (2015); Schindler et al. (2016) Lake Restoration
    Nov. 11 (F, 1:30)                            

Contaminants in Aquatic Systems

Week 10   Nov. 15 (Tu, 12:30)                           

Guest Lecture - Contaminants

    Lab 5, Group 1                 

Lab 5 (Group 1) – Microcosms; Assignment 2 (Lab 4) due Group A

    Nov. 17 (Th, 11:30)                              Guest Lecture - Invasive Aquatic Species

Nov. 18 (F, 1:30)                            

  Lakes and Climate
Week 11  

Nov. 22 (Tu, 12:30)                           

  Multiple Stressors in Tropical Lakes
    Lab 5, Group 2   Lab 5 (Group 2) – Microcosms; Assignment 2 (Lab 4) due Group B

Nov. 24 (Th, 11:30)                           


  Guest Lecture - Arctic and Antarctic Lakes

Nov. 25 (F, 1:30)                            

  Guest Lecture - Fish and Climate
Week 12   Nov. 29 (Tu, 12:30)                         
  USAT + Lake Ontogeny
    Dec. 1 (Th, 11:30)                  Review Session - please come with questions
  Lab Exam Dec. 2 (F, 1:30); or 2:30 (for those in Friday Lab)   Lab Exam - bell ringer
Exam Period Final Exam TBA Link to past exams 50% short answer/ 50% essay

*note: assignments are due in your regularly scheduled lab slot.


If you would not be forgotten,
as soon as you are dead and rotten,
either write things worth reading,
or do things worth the writing.

Benjamin Franklin, Poor Richard's Almanac (1738)

One of the skills you are expected to master during your university education is to communicate clearly and logically the knowledge that you have gained.  Therefore, two written assignments are part of this course.  As 25% of your final mark will be dependent on them, you should spend considerable time in preparing concise, clear and correct reports.  These reports should be written as papers. The format of the papers will be detailed in your lab. Reports are due by the beginning of your next laboratory (i.e. you have two weeks to complete them).  Marks will be reduced by 5% for each day a report is late (weekends will count as a single day).  We will not be able to accept the excuse of a disk or a hard-drive crashing (make back-up copies!!).

Labs are held every other week, starting in the second week.  PDF files of the labs, and the compulsory field day at the Queen’s University Biological Station are found below. Please come prepared for the labs (i.e., Please read and understand the PDF for the lab).  Attendance at the labs is compulsory. If you miss a lab without a valid excuse, your assignment will not be marked. 

Links to PDF files and readings for labs:

Lab 1 (Lake Models): |Lab 1|
Fieldtrip: |Fieldtrip|
Lab 2 (Chemical Techniques): |Lab 2|
Lab 3 (Phytoplankton and Zooplankton): |Lab 3|
Lab 4 (Paleolimnology Lab): |Lab 4|
Lab 5 (Microcosms): |Lab 5|


Academic Integrity and Queen’s Code of Conduct

Academic integrity is constituted by the five core fundamental values of honesty, trust, fairness, respect and responsibility. These values are central to the building, nurturing and sustaining of an academic community in which all members of the community will thrive. Adherence to the values expressed through academic integrity forms a foundation for the "freedom of inquiry and exchange of ideas" essential to the intellectual life of the University.

Students are responsible for familiarizing themselves with the regulations concerning academic integrity and for ensuring that their assignments and conduct conform to the principles of academic integrity. Information is available in the Arts and Science Calendar (see Academic Regulation 1 -, on the Arts and Science website (see, and at Biology’s website (
and from the instructor of this course. Departures from academic integrity include plagiarism, use of unauthorized materials, facilitation, forgery and falsification, and are antithetical to the development of an academic community at Queen's. Given the seriousness of these matters, actions which contravene the regulations on academic integrity carry sanctions that can range from a warning or the loss of grades on an assignment to the failure of a course to a requirement to withdraw from the university.

Accommodation Policy, Exam Conflicts, and Other Conflicts

Students who feel they need accommodations for disabilities or extenuating circumstances, or have a conflict between exams or other commitments should consult the Biology Department’s website for details about how to proceed ( In general, the earlier a course coordinator is apprised of an extenuating circumstance, the more likely an accommodation can be made. Students are encouraged to be proactive in anticipating difficulties, when it is possible to do so.

Students may apply to write a make-up or deferred exam if they have an exam conflict as defined in the Academic Regulations of the Faculty (See Arts and Science Calendar Regulation 8 - In this case, the student should report to the Exams Office first to verify that there is a genuine exam conflict. Biology professors will not consider your situation to be a conflict unless it meets the criteria set out by the Faculty of Arts and Sciences.
Students may request a make-up or deferred exam if they have an exam conflict with off-campus travel associated with a field course (e.g., BIOL-307/3.0 or 407/3.0) that is held during the fall or winter terms.

This material is designed for use as part of BIOL 335  at Queen’s University and is the property of the instructor unless otherwise stated. Third party copyrighted materials (such as book chapters and articles) have either been licensed for use in this course or fall under an exception or limitation in Canadian Copyright law.

Accommodation of Disabilities
Queen's University is committed to achieving full accessibility for persons with disabilities. Part of this commitment includes arranging academic accommodations for students with disabilities to ensure they have an equitable opportunity to participate in all of their academic activities. If you are a student with a disability and think you may need accommodations, you are strongly encouraged to contact the Disability Services Office (DSO) and register as early as possible. For more information, including important deadlines, please visit the DSO website at: