Ecosystem Metabolism

2015 Short Course: Methods and models for estimating aquatic ecosystem metabolism

Umeå University, Umeå, Sweden

Spring 2015

Contact Erin Hotchkiss (ehotchkiss[at] for Methods in Stream Ecology chapter that emerged from these lessons and other collaboraitons

Part 1 - Introduction to aquatic ecosystem metabolism: History and methods

Additional references:

Part 2 - Introduction to Likelihood and Bayesian

Additional references:

Part 3 - Aquatic ecosystem metabolism models: Structure, complexity, and parameter estimation

Additional references:

Part 4 - Review R code for Likelihood and Bayesian 1-station metabolism models

On your own: run original code for 1 day of metabolism estimates using (1) Likelihood and (2) Bayesian parameter estimation. Update the R code to run for several days of O2 data from three different streams using "guidelines" handout. Reflect on the additional questions provided.

Part 5 - Review, quality check, and compare output from Likelihood and Bayesian metabolism models

2010 Workshop: Inverse Modeling Methods for Estimating Aquatic Ecosystem Metabolism

American Society of Limnology & Oceanography

North American Benthological Society

Date: 06 June 2010

Time: 13:00 - 17:00

Location: Peralta/Lamy, Santa Fe Conference Center

RSVP to: Bob Hall (bhall[at] & Erin Hotchkiss (ehotchki[at]

Workshop Description:

There is a current increase in interest in calculating aquatic whole-ecosystem metabolism using inverse modeling approaches. In some cases it is possible to solve for more than just metabolism; reaeration can be estimated, which allows broad application of the method, but at a possible cost of higher uncertainty in metabolism estimates.

This workshop will discuss methods, models, and assumptions behind inverse approaches to estimating aquatic ecosystem metabolism. Questions will include how to both calculate and minimize uncertainty on parameter estimates (i.e. photosynthesis, respiration, reaeration) and how many parameters can be estimated with low uncertainty given variation in diel oxygen or oxygen isotope data. We envision a session with a few short presentations addressing modeling of metabolism, followed by small or large group discussions on specific questions.

The overall goal of the workshop will be to develop recommendations for modeling metabolism, including parameter estimation and uncertainty. 

Specific questions:


12:40 - Load presentations onto computer

Part 1. Methods used to estimate aquatic metabolism

13:00 - Workshop introduction: Goals, questions, and a little data (Bob Hall)

13:17 - Estimating metabolic parameters from one- and two-station diel dissolved oxygen curves: Successes and challenges (Mike Grace)

13:34 - Estimating metabolism parameters and uncertainty: maximum likelihood approach with bootstrapping (Christopher Solomon, Matthew Van de Bogert, & Paul Hanson)

13:51 - Bayesian methods for aquatic ecosystem metabolism parameter estimation: current models and future directions (Gordon W. Holtgrieve & Daniel E. Schindler)

14:08 -Sampling more places less frequently: What increase in error are we to accept for better spatial coverage? (Jason Venkiteswaran)

14:25 - Revised techniques for estimating stream metabolism from oxygen concentrations: The effect of spatial heterogeneity (Peter Reichert, Urs Uehlinger, & Vicenç Acuña)

14:42 - Estimates of stream metabolism by modeling dissolved oxygen fate and transport in unsteady flow (Robert Payn)

15:00 - 15 minute break

Part 2. Small group discussion and recommendations

15:15 - Break out into small groups for more focused discussions:

    1. Measuring versus modeling K

    2. Parameter uncertainty

    3. Model structure and model validation

    4. Others?

16:15 - Groups report recommendations; large group discussion

16:40 - Workshop summary: Recommendations and future directions (Erin Hotchkiss)