BIOLOGY 335*            LIMNOLOGY AND AQUATIC ECOLOGY (Fall 2018)           

|Course Information| |Lecture Schedule and links to PDF Files| |Labs, Fieldtrip & Assignments| |Cumming 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 and Head, Biology; Cross-appointed: School of Environmental Studies

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

Teaching Assistants (TAs):

Cecilia Barouillet---------Graham Mushet------Brigitte Simmatis; Graham Mushet <>; Brigitte Simmatis <>

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 3-unit course we cannot attempt to consider all facets of limnology in depth.  However, we will 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, and solutions to pressing problems in aquatic ecology.

More specifically the Learning Outcomes of this course include being able to:

a) Explain and effectively communicate how basic principles and concepts associated with the physical, chemical, and biological aspects of limnology can be applied to understand lake ecosystems;
b) Understand, recognize and describe contributions from the disciplines of physics, chemistry, biology, geography, environmental studies and engineering to the understanding of limnological systems;
c) Use limnological techniques to collect, analyse and interpret chemical and biological data;    
d) Conduct, analyse and interpret the laboratory exercises to gain understanding of limnological concepts, and gain experience in the writing of clear, concise and integrated reports;
e) Apply limnological concepts and critical thinking to demonstrate an integrated understanding of the roles of physical, chemical and biological characteristics and processes in structuring aquatic communities (at all trophic levels from microbes to fish), in Arctic, temperate and tropical systems; and
f) Describe, understand, logically predict, and clearly communicate the impact of a variety of human activities (e.g. watershed disturbances, mining, industrial activities) on ecosystems and environmental health, and formulate appropriate remediation techniques.

Course material will be presented by three approaches ‑ in formal lectures, laboratories, and a compulsory one-day (either Saturday, September 29th, or Sunday, September 30th) 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 office (Rm. 3102) in the Biosciences Complex (613 533-6153).

Lectures: Monday (10:30-11:20), Wednesday (9:30 -10:20) and Friday (8:30 - 9:20), Jeffery Hall, Rm. 225.

Labs:Total of 4 labs + one-day compulsory fieldtrip (Saturday, September 29th or Sunday, September 30th).

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

Lab times: Sections: Monday 2:30 to 5:30 pm; Wednesday, 11:30-2:30 pm; Friday, 11:30-2:30 pm. 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, September 29, or Sunday, September 30th. 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  

Marking Scheme:
A) Assignment 1:  Lake Models (Lab 1) - 10%;
B) Midterm exam - 20% - covers lecture material upto the end of the Physical and Chemical Limnology section of this course
C) Assignment 2:  Paleoecology (Lab 3) - 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, but with the expectation of integrating the material learned in the first part of the course. .


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

PLEASE NOTE: These powerpoint slides 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 to develop.

Links to PDF files for labs:

Lab 1 (Lake Models): |BIOL335Lab 1|
Fieldtrip: |BIOL335Fieldtrip|
Lab 2 Chemical Techniques, phytoplankton and zooplankton|BIOL335Lab 2|
Lab 3 (Paleolimnology Lab): |BIOL335Lab 3|
Lab 4 (Microcosms): |BIOL335Lab 4|

  Lecture Topic Date (day) Lab Times Lab Due Date


(Chapters in Wetzel)

Lecture Topic
Week 1 Introduction and Physical Limnology                 Sept. 7 (F, 8:30)     1,2,5                     

Introduction, properties of water and light

Week 2


Sept. 10 (M ,10:30) Lab Introduction   6           

Heat and Lake Stratification


Sept. 12 (W, 9:30) 

Lab Introduction     PDF Lewis             

Lake Classification: the influence of climate and basin shape

    Sept. 14 (F, 8:30) Lab Introduction   3 Origin of Lakes
Week 3   Sept. 17 (M, 10:30)

Lab 1, Group A

  7 Water Movements
  Chemical Limnology Sept. 19 (W, 9:30)   Lab 1, Group A                       Oxygen

Sept. 21 (F, 8:30)  

Lab 1, Group A

  10                 Salinity
Week 4  

Sept. 24 (M, 10:30) 

Lab 1, Group B   11 Inorganic Carbon
    Sept. 26 (W, 9:30)     12

Nitrogen Cycle

    Sept. 28 (F, 8:30)                              
Lab 1, Group B  

13, Orihel et al. 2017. Internal phosphorus loading in Canadian freshwaters: a critical review and data analysis.

Phosphorus Cycle
  Opinicon Fieldtrip Sept 29 (Sat) or Sept. 30(Sun): 7:20 am to 6 pm     List showing day of your fieldtrip Field manual (please read before field day)
Week 5   Oct 1 (M, 10:30) NO LAB   14 Micronutrients (S, Si)
    Oct 3 (W, 9:30) NO LAB     Case Study - Lake Nyo
  Primary/ Secondary Production Oct. 5 (F, 8:30)       NO LAB   8,15 Introduction to Algae and Algal Ecology
Week 6  

Oct. 8 (M) - Thanksgiving (no class)

NO LAB     No Class
    Oct. 10 (W, 9:30)  
Lab 2, Group A Lab 1 due Example Midterm    MIDTERM (in class) 2018 Miderm with answers

Oct. 12 (F, 8:30)                              

Lab 2, Group A Lab 1 due 15 Ecology and Seasonality of Algae
Week 7   Oct. 15 (M, 10:30) Lab 2, Group A Lab 1 due 16 Introduction to Zooplankton


Oct. 17 (W, 9:30)      

Fish and Trophic Interactions
  Integrative Limnology

Oct. 19 (F, 8:30)

Lab 2, Group B Lab 1 due 24            Introduction ot Paleolimnology
Week 8  

Oct. 22 (M, 10:30)     

Lab 2, Group B Lab 1 due               Lake Acidification

Oct. 24 (W, 9:30)

    Cumming et al. 1992; Cumming et al. 1994              Applied Paleolimnology: Acidification of the Adirondacks
    Oct. 25,26 (F) - FALL BREAK - no class or lab    


Week 9   Oct. 29 (M, 10:30) Lab 3, Group A  

Meyer-Jacob et al. 2017. Inferring past trends in lake water organic carbon concentrtations in northern lakes using sediment spectroscopy

C. Meyer-Jacob - Past trends in organic carbon from lake sediments.

Please see link to the left. This lecture provides important background information for Lab 3.

     Oct. 31 (W, 9:30)     
Lab 3, Group A   Arseneau et al. 2016.  Adirondack reference lakes show pronounced shift in chrysophyte species composition ca. 1900 Multiple stressors and reference sites
    Nov 2 (F, 8:30)                             Lab 3, Group A     Lake Restoration
Week 10  

Nov 5 (M, 10:30)                               

Lab 3, Group B     Contaminants in Aquatic Systems

Nov. 7 (W, 9:30)                             

      T. Laing - Contaminants in Kingston's Inner Harbour

Nov. 9 (F, 8:30)                        

Lab 3, Group B   Smol and Cumming. 2001. Tracking long-term changes in climate using algal indicators in lake sediments. Lakes and Climate
Week 11   Nov. 12 (M, 10:30)                            
Lab 4, Group A Lab 3 due Verschuren et al. 2002. History and timing of human impact on Lake Victoria, East Africa.

Multiple Stressors in Tropical Lakes

    Nov. 14 (W, 9:30)                           
Lab 4, Group A Lab 3 due

Kidd, K.A. et al. 2007. Collapse of a fish population following exposure to a synthetic estrogen.
Kidd, K.A. et al. 2014. Direct and indirect responses of a freshwater food web to a potent synthetic estrogen. 
Blanchfield, P.J. et al. 2015. Recovery of a wild fish population from whole-lake additions of a synthetic estrogen.
Palace, V.P. et al. 2009. Interspecies differences in biochemical, histopathological, and population responses in four wild fish species exposed to ethynylestradiol added to a whole lake. 

P. Blanchfield - Endocrine Disruptors

    Nov. 16 (F, 8:30)                         Lab 4, Group A Lab 3 due   S. Arnott - Invasive Aquatic Species
Week 12  

Nov. 19 (M, 10:30)                            

Lab 4, Group B Lab 3 due   J.M.Casselman - Fish and Climate

Nov. 21 (W, 9:30)                           

      C. Barouillet and M. Duda - cool studies at PEARL



Nov. 23 (F, 8:30)                           


Lab 4, Group B Lab 3 due   J. Smol - Polar Lakes
Week 13 Lab Exam

Nov. 26 (M)    

10:30 for those not in Monday Lab; 2:30 for those in Monday lab                        

Lab Exam   Study guide from Sunny Lee Lab Exam - bell ringer
    Nov. 28 (W, 9:30)                         
      USAT + Lake Ontogeny
    Nov. 30 (F, 8:30)                  Review session - come with questions
Exam Period Final Exam Dec. 20 (9:00) - Ross Gym     Link to past exams 50% short answer/ 50% essay

*note: labs 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 (Lab 1 and Lab 3).  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).  Please be sure to backup your data.

The schedule for the labs is posted in the schedule above. Show up to your first lab. You will be assigned to be in either the A or B section of the lab. PDF files of the labs, and the compulsory field day at the Queen’s University Biological Station can be found above. Please come prepared for the labs (i.e., 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. 


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 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:

Academic Accommodations are term-long accommodations that are managed by Queen’s Student Accessibility Services. Typical accomodations may include extra time on assessments and/or special room requirements. At the beginning of the term, the student send the me a copy of your Letter of Accommodation, and accomodations will be made.

Academic Consideration is mitigation for a short-term issue related to an extenuating circumstance. All academic considerations must go through the student portal available on the Faculty of Arts and Science website ( Following your request, I will be notified.

There are 2 types of academic considerations. The first is called a ‘brief absence’ (up to 48hrs) and is essentially a self-declaration of an extenuating circumstance. The second is a short-term extenuating circumstance that can be from 2 days-3 months. The later requires documentation.

The aim of centralizing academic considerations is to log extenuating circumstances to provide better support for students who need it, and to watch for patterns where students are abusing the system.

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.