(Input data for) RiverMET: Workflow and scripts for river metabolism estimation including Illinois River Basin application, 2005 - 2020
Dates
Publication Date
2022-05-09
Start Date
2005-10-01
End Date
2020-12-31
Citation
Choi, J., Quion, K.M., Reed, A.P., and Harvey, J.W., 2022, RiverMET: Workflow and scripts for river metabolism estimation including Illinois River Basin application, 2005 - 2020: U.S. Geological Survey data release, https://doi.org/10.5066/P9TEBOUR.
Summary
Ecosystem metabolism is a measure of energy flow in terrestrial and aquatic environments that quantifies a balance between the rate of biomass production by photosynthesizing plants and the rate of biomass oxidation by respiring plants and animals to maintain and build living biomass. It is therefore a fundamental measure of ecosystem function that quantifies the balance between the rate of production, maintenance, and decay of organic matter. It also provides an understanding of energy flow to higher trophic levels that supports food webs with secondary and tertiary productivity. Furthermore, metabolism helps explain when aquatic ecosystems undergo out-of-balance behaviors such as hypoxia. Recent advances in sensor technology and [...]
Summary
Ecosystem metabolism is a measure of energy flow in terrestrial and aquatic environments that quantifies a balance between the rate of biomass production by photosynthesizing plants and the rate of biomass oxidation by respiring plants and animals to maintain and build living biomass. It is therefore a fundamental measure of ecosystem function that quantifies the balance between the rate of production, maintenance, and decay of organic matter. It also provides an understanding of energy flow to higher trophic levels that supports food webs with secondary and tertiary productivity. Furthermore, metabolism helps explain when aquatic ecosystems undergo out-of-balance behaviors such as hypoxia. Recent advances in sensor technology and modeling capabilities have enabled estimation of aquatic system metabolism and gas exchange over long time periods in rivers, streams, ponds, and wetlands where oxygen sensors have been deployed.
For convenience, metabolism can be measured by tracking the rate of oxygen production and consumption in the aquatic system. Over time, the measurements of dissolved oxygen concentration can be analyzed to estimate both gross primary productivity (GPP) and ecosystem respiration (ER). GPP is defined as positive, adding oxygen and organic carbon to the system, and ER is defined as negative, subtracting oxygen by consuming organic carbon to fuel work. The sum of GPP and ER is the net ecosystem productivity, a net measure of whether oxygen and organic carbon are building up or being depleted in the system. In order to use the oxygen balance method to quantify GPP and ER in shallow waters it is also necessary to quantify the rate of gas exchange with the atmosphere by accounting for physical effects of surface renewal as well as the dissolved oxygen difference compared to the saturated concentration for a given temperature and atmospheric pressure.
Here we present RiverMET for estimating river metabolism with provided workflows that streamline data preparation, run a metabolism model, assess the model performance, and flag and censor final output data. We tested RiverMET by calculating gross primary productivity (GPP), ecosystem respiration (ER) and the air-water gas exchange rate constant (K600) across seventeen (17) river sites in the Illinois River basin (ILRB) using water quality data and hydrologic data from National Water Information System (NWIS, https://waterdata.usgs.gov/nwis, data accessed September 2021) and pressure data from National Oceanic and Atmospheric Administration (NOAA, https://www.ncei.noaa.gov/maps/lcd/, data accessed September 2021). The workflows are specifically tailored to use streamMetabolizer (version 0.12.0; https://github.com/USGS-R/streamMetabolizer), a model for one-station calculations of stream metabolism that calculates daily average areal rates of GPP and ER, and the daily average volumetric air-water gas exchange rate constant, K600. We advise potential users of RiverMET to review core publications for the streamMetabolizer model to ensure best practices that produce the most useful results. We encourage feedback about our workflows, although issues regarding the streamMetabolizer model itself should be referred to the model authors.
The zipped (.zip) folder "RiverMET_Inputs.zip" contains five (5) comma-separated value (.csv) files of field observations and one (1) text (.txt) file containing hydraulic geometry coefficients collectively used to run the streamMetabolizer model (version 0.12.0) across the seventeen (17) sites within the Illinois River Basin. The format is standardized across each of the .csv files and includes USGS Site Number, Date/Time, and the values of the parameter(s) unique to the .csv file. Raw data was processed to the format and time interval suitable for the streamMetabolizer model (version 0.12.0). Before executing streamMetabolizer model (version 0.12.0), all input data was validated by comparing with the raw downloaded data.
This work was completed as part of the U.S. Geological Survey Proxies Project, an effort supported by the Water Mission Area (WMA) Water Quality Processes program to develop estimation methods for, harmful algal blooms (HABs), per- and polyfluoroalkyl substances (PFAS), and metals, at multiple spatial and temporal scales.
