Data Package Metadata   View Summary

Multispectral absorbance and fluorescence analysis of dissolved organic carbon in water samples taken from the Upper Clark Fork River (Montana, USA) during water years 2017 and 2018 (1 Oct 2016 - 30 Sep 2018)

General Information
Data Package:
Local Identifier:edi.410.11
Title:Multispectral absorbance and fluorescence analysis of dissolved organic carbon in water samples taken from the Upper Clark Fork River (Montana, USA) during water years 2017 and 2018 (1 Oct 2016 - 30 Sep 2018)
Alternate Identifier:DOI PLACE HOLDER
Abstract:

The Upper Clark Fork River (UCFR) Long Term Research in Environmental Biology (LTREB) umbrella monitoring project generating these data is conducted separately and complementarily to the 200-million-dollar (USD) superfund project for ecological restoration of the UCFR, associated tributaries, and head water streams including Silver Bow and Warm Springs Creeks. Restoration along the UCFR in western Montana includes removal of metal-laden floodplain soils, lowering of the floodplain to its original elevation, and re-vegetation of over 70 km of the river’s floodplain closest to contaminant sources. The UCFR LTREB project includes bi-weekly water quality monitoring across the first 200 km of the river and its major tributaries along a gradient of heavy metal contamination associated with historic mining. Monitoring includes inorganic phosphorus and nitrogen concentrations, biotic standing stocks, and dissolved and whole-water heavy metal concentrations. The monitoring program began in 2017 with funding likely to be extended through 2028. The original analytical intent for these data was to assess the response of river dissolved organic carbon to the floodplain restoration. Data are multispectral absorbance and fluorescence analyses of organic carbon dissolved in samples of well-mixed river thalweg water. Data include excitation-emission matrices, absorbance spectroscopy, as well as absorbance and fluorometric summary indices calculated at specific wavelengths of excitation and emission. Data are from the 2017 and 2018 water years (1 Oct 2016 to 30 Sep 2018). Data were collected on the Upper Clark Fork River (USGS HUC 17010201) at 13 project sites distributed along the river from the vicinity of Anaconda to Missoula, Montana, USA.

These data are a correction of a previously published data product (doi:10.6073/pasta/6ba30f4ebb63175a4399c5d0aa6a8698). Inconsistencies between availability of EEMS data, absorbance data, and fluorometric summary metrics have been corrected. Part of resolving these inconsistencies included correcting the year on a limited number of the records in the fluorometric summary metric table.

Purpose:
Water quality in the Upper Clark Fork River (UCFR) suffers from a century-old mining legacy. Heavy metals and nitrogen enrichment associated with human activity influence aquatic communities and processes. A 200-million-dollar (USD) ecological remediation and restoration of the UCFR was initiated in 2013 and will continue for 20 years. Large-scale ecological restoration of the UCFR floodplain after removal of mine waste contamination is a component of the largest US EPA “superfund” project since implementation of the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) by the US government in 1980. Remediation of the uppermost 70 km of the UCFR is removing metal-contaminated sediments while restoration includes restructuring the floodplain and its vegetation while lowering its elevation to promote interaction with the river during high flows. Upgrades to wastewater treatment plants and changing hydrologic conditions will occur even as the State of Montana embarks upon a whole-scale restoration of the UCFR floodplain. Since the 1990s, state agencies and University of Montana (UM) researchers have gathered data on the benthic algae, river water chemistry, and sediment transformation of contaminants in water. UCFR LTREB funds starting in 2017 have continued support of baseline monitoring of metal contamination, carbon, biomass, nutrients, and metabolic activity. The motivation for extending the long-term dataset is to address changes in the character of subsidies and stressors for river productivity, algal blooms, and ecological integrity in a river being restored from long-term contamination problems. of generating the data product.
Publication Date:2023-07-18
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
2017-08-15
End:
2018-09-27

People and Organizations
Contact:D'Andrilli, Juliana (Louisiana Universities Marine Consortium) [  email ]
Creator:D'Andrilli, Juliana (Louisiana Universities Marine Consortium)
Creator:Valett, H Maurice (University of Montana)
Creator:Utzman, Claire (University of Montana)
Associate:D'Andrilli, Juliana (Louisiana Universities Marine Consortium, Funding Acquisition; Conceptualization; Supervision; Investigation; Methodology; Formal Analysis; Data curation)
Associate:Valett, H Maurice (University of Montana, Funding Acquisition; Conceptualization)
Associate:Utzman, Claire (University of Montana, Investigation)
Associate:Junker, James R (Michigan Technological University, Formal Analysis; Data curation)
Associate:Bayrd, Venice (Montana State University, Data curation)
Associate:Payn, Robert A (Montana State University, Funding Acquisition; Conceptualization; Data curation)
Associate:Hurley, Patrick (University of Montana, Investigation)
Associate:Peipoch, Marc (Stroud Water Research Center, Funding Acquisition; Conceptualization)
Associate:DeGrandpre, Michael D (University of Montana, Funding Acquisition; Conceptualization)

Data Entities
Data Table Name:
EEMS_wy2017-18_Aqualog.csv
Description:
References to comma delimited text files with analysis-ready excitation-emission matrices (EEMS) from fluorometric analysis of dissolved organic carbon sampled in triplicate along the Upper Clark Fork River.
Data Table Name:
EEMS_excitation_wavelengths.csv
Description:
Wavelenths for excitation (columns left to right) in EEMS matrices
Data Table Name:
EEMS_emission_wavelengths.csv
Description:
Wavelenths for emissions (rows top to bottom) in EEMS matrices
Data Table Name:
Absorbance_wy2017-18_Aqualog.csv
Description:
Absorbance for all excitation wavelengths from analysis with an Aqualog multispectral fluorometer
Data Table Name:
Summary_metrics_wy2017-18.csv
Description:
Summary metrics of absorbance and fluorescence including the absorbace at 254nm, fluorescence index, and humification index
Other Name:
EEMS_wy2017-18_Aqualog_matrices.zip
Description:
Compressed zip file with fluorometric excitation-emission matrices. Matrix columns represent excitation wavelengths and matrix rows represent emission wavelengths (see Methods for details). Files are indexed by sampling date, site ID, and replicate ID in the table EEMS_wy2017-18_Aqualog.csv.
Other Name:
Summary_metrics_wy2017-18_vis.pdf
Description:
Visualization of the absorbance and fluorescence summary metrics over time.
Other Name:
01_input.zip
Description:
Compressed data pipeline folder containing project default metadata. See methods for details.
Other Name:
02_protocol.zip
Description:
Compressed data pipeline folder containing R markdown and R scripts for processing data and metadata. See methods for details.
Other Name:
03_incremental.zip
Description:
Compressed data pipeline folder containing detailed notes and incremental data associated with generation of the data product. See methods for details.
Other Name:
readme.html
Description:
Detailed description of the data product
Detailed Metadata

Data Entities


Data Table

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repID  
wavelength  
absorbance  
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siteID  
repID  
abs_254  
FI  
HIX  
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Data Package Usage Rights

Intellectual rights to the data of this data package are treated separately to the code; please read carefully below. Professional etiquette dictates attribution of the original work if this data package is shared in whole or by individual components. A generic citation is provided for this data package on the website https://portal.edirepository.org (herein "website") in the summary metadata page. Communication (and collaboration) with the creators of this data package is recommended to prevent duplicate research or publication. This data package (and its components) is made available "as is" and with no warranty of accuracy or fitness for use. The creators of this data package and the website shall not be liable for any damages resulting from misinterpretation or misuse of the data package or its components. Periodic updates of this data package may be available from the website. Thank you. ## CODE LICENSE STATEMENT Copyright 2022 - Robert Payn The code files presented here are available under the MIT License. The full Legal Code text is available below, and also here: https://opensource.org/licenses/MIT. Specific files released under this license include: - *02\_protocol.zip* - *.Rprofile* - *01\_processing.Rmd* - *01\_processing\_compile.R* - *10\_metadata.Rmd* - *10\_metadata\_compile.R* - *RStudioProject.Rproj* ### Legal Code Text - MIT License Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 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Keywords

By Thesaurus:
(No thesaurus)Upper Clark Fork River restoration, NSF DEB LTREB 1655197, Montana, Northwestern United States, Northwestern Forested Mountains Ecoregion, excitation-emission matrix
NALTriver water, fluorescence, absorbance, spectroscopy
LTER Controlled Vocabularydissolved organic carbon

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:
## Previous versions These data are a correction of a previously published data product (doi:10.6073/pasta/6ba30f4ebb63175a4399c5d0aa6a8698). Inconsistencies between availability of EEMS data, absorbance data, and fluorometric summary metrics have been corrected. Part of resolving these inconsistencies included correcting the year on a limited number of the records in the fluorometric summary metric table. ## Measurement methods Where more details are available, each description below is cross-referenced with the brief methods caption provided in the descriptions of the table columns. ### *Field sample management protocol*: Water samples were collected from the thalweg using a 4-L HDPE bottle. Filtration was conducted with an apparatus that included a Millipore filter holder with a filtrate collection vessel, Whatman glass fiber filters (pore size 0.7 micron), and a 12-V Thomas vacuum pump. Before sampling, filters were combusted at 500 degrees Celsius for one hour. Filtered water from this unit was placed into a 20-milliliter borosilicate amber glass vial, which before sampling was acid-washed and combusted at 425 degrees Celsius for 4 hours. Filtered water was used to rinse the vials before being filled. Vials were capped with a lid containing a Teflon disc. Samples were stored on ice in a cooler in the dark in transport to the lab and subsequently stored in a refrigerator at ca. 4 degrees Celsius before analysis. ### *Aqualog multispectral fluorometry*: Fluorescence of aqueous samples was measured in the W.A. Franke College of Forestry & Conservation Ecosystems Lab (directed by Dr. Benjamin Colman) at the University of Montana using an Aqualog Multispectral Fluorometer (Horiba, Kyoto, Japan). Filtered samples of river water are exposed to radiation at excitation wavelengths from 240 to 450 nanometers at a 5-nanometer resolution. Excitation wavelengths correspond to the columns of the excitation-emission matrices provided in this data product. The fluorometric intensity of the emission wavelengths are measured from 300 to 560 nanometers at a 2-nanometer resolution. Emission wavelengths correspond to the rows of the excitation-emission matrices provided in this data product. Values provided in the excitation-emission matrices are thus fluorometric intensities of emission at a given pairing of excitation and emission wavelengths as indicated by the column and row in the matrix. All data were generated in signal/reference mode to normalize the emission signal relative to the excitation light intensity. EEMs were corrected using Aqualog-specific protocols outlined in Cory et al. (2010). Spectra were corrected against purified water (Milli-Q) field blanks that were exposed to the same sampling protocol as stated in the field sample management protocol above. One blank sample was collected per sampling day. UV-Vis absorbance spectra from each scan were used to correct the EEMS for the inner filter effects and scattering corrections were applied for the Rayleigh-Tyndall effect and Raman scattering peaks. The fraction of the excitation radiation absorbed by the sample at each wavelength is also measured by the fluorometer. Absorbance was interpolated from the 5-nm excitation resolution to a 1-nm resolution of absorbance values. This interpolation is necessary to estimate absorbance values at wavelengths commonly used for summarizing organic matter quality, such as 254 nm. ### *Fluorescence index derivation*: After fluorometric excitation at a wavelength of 370 nm, the fluorescence index (FI) is calculated as the ratio of the fluorescence emission intensity at 450 nm divided by the fluorescence emission intensity at 500 nm (McKnight et al. 2001). ### *Humification index derivation*: After fluorometric excitation at a wavelength of 254 nm, the humification index (HIX) is calculated by dividing the sum of fluorescence intensities between emission wavelengths 435 and 480 nm by the sum of fluorescence intensities between emission wavelengths 300 and 345 nm (Ohno, 2002). Numbers reported are relative to the corresponding absorbance of a blank sample, such that negative numbers indicate an absorbance less than that of the blank. ## Data processing methods This data product is designed to provide the provenance of final tables in a pipeline format, to the degree that provenance is available. Raw data files from instruments and manufacturer software are available in the 01\_input.zip file. The coding used to process the data is available in the 02\_protocol.zip file. In this case, final processing was carried out with R scripts and R markdown files. Incremental files created for the purpose of data processing are available in the 03\_incremental.zip file. Ready-to-use analytical data are available at the data package's root level (on the dataset landing page under the "Resources" section) and are described in the full metadata. ### *Contents of 01\_input.zip* - *meta/* - Directory with project templates for metadata - *2021 Site Table.xlsx* - Microsoft Excel file with authoritative project site list at the time of publication of these data. - *attributes.xlsx* - Excel file with commonly used table column attributes in the project - *narr\_abstract.md* - Markdown text file with abstract - *narr\_methods.md* - Markdown text file with methods - *narr\_purpose.md* - Markdown text file with purpose statement - *narr\_rights.md* - Markdown text file with intellectual rights - *narr\_title.txt* - Text file with title - *people.xlsx* - Excel file with tabular data on people associated with the project used for metadata generation. - *ppl\_contact.csv* - Comma delimited text file with contact information - *ppl\_creators.csv* - Comma delimited text file with list of creators - *ppl\_funding.csv* - Comma delimited text file with list of funders - *ppl\_others.csv* - Comma delimited text file with list of other contributors ### *Contents of 02\_protocol.zip* R code in this folder depends on external R packages: knitr, readxl, rmarkdown, xml2, EMLassemblyline, and shiny. Code also makes system calls to the zip command using arguments compatible with Info-Zip implementation 3.0, which appear to be mostly consistent with linux zip arguments. - *.RProfile* - An R profile file with R code that establishes the appropriate working directory for the R project used to generate this data product. - *01\_processing.Rmd* - R markdown creating the data tables and associated metadata. - *01\_processing\_compile.R* - R script that compiles the processing R markdown to an HTML document (*03\_incremental.zip/processing\_notes.html*) - *10\_metadata.Rmd* - R markdown defining the generation of the metadata file and the EML file based on EDI EML assembly line. - *10\_metadata\_compile.R* - R script that compiles the metadata R markdown to an HTML document (metadata.html) and an EML file (eml.xml). - *RStudioProject.Rproj* - An RStudio project file provided for convenience in working with the code generating this data product with the appropriate working directory. ### *Contents of 03\_incremental.zip* R code included in this product will generate temporary files in the ./03\_incremental/Temp folder. These temporary files contain no unique data or metadata and thus are not archived in the corresponding zip file. - *eemsFilenames\_2017.RData* - RData file with the incremental copy of the sorted EEMS file names for generating the cross-reference table - *eemsFilenames\_2018.RData* - RData file with the incremental copy of the sorted EEMS file names for generating the cross-reference table - *LTREB\_OpticalProp\_Aqualog\_WY\_2017\_FINAL.csv* - Original data file for summary metrics. - *LTREB\_OpticalProp\_Aqualog\_WY\_2018\_FINAL.csv* - Original data file for summary metrics. - *processing\_notes.html* - Metadata regarding the processing of the raw data files to the product's data tables and basic visualizations. ## References Cory, R. M., M. P. Miller, D. M. McKnight, J. J. Guerard, and P. L. Miller. 2010. Effect of instrument-specific response on the analysis of fulvic acid fluorescence spectra. Limnology and Oceanography-Methods 8(2) 67-78. McKnight, D. M., E. W. Boyer, P. K. Westerhoff, P. T. Doran, T. Kulbe, and D. T. Andersen. 2001. Spectrofluorometric characterization of dissolved organic matter for indication of precursor organic material and aromaticity. Limnology and Oceanography 46(1) 38-48. Ohno, T. 2002. Fluorescence inner-filtering correction for determining the humification index of dissolved organic matter. Environmental Science and Technology, 36, 742-746.

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@edirepository.org
Web Address:
https://edirepository.org
Id:https://ror.org/0330j0z60
Creators:
Individual: Juliana D'Andrilli
Organization:Louisiana Universities Marine Consortium
Email Address:
jdandrilli@lumcon.edu
Id:https://orcid.org/0000-0002-3352-2564
Individual: H Maurice Valett
Organization:University of Montana
Email Address:
Maury.Valett@mso.umt.edu
Id:https://orcid.org/0000-0001-7146-6420
Individual: Claire Utzman
Organization:University of Montana
Email Address:
claire.utzman@mso.umt.edu
Id:https://orcid.org/0000-0002-3228-8470
Contacts:
Individual: Juliana D'Andrilli
Organization:Louisiana Universities Marine Consortium
Email Address:
jdandrilli@lumcon.edu
Id:https://orcid.org/0000-0002-3352-2564
Associated Parties:
Individual: Juliana D'Andrilli
Organization:Louisiana Universities Marine Consortium
Email Address:
jdandrilli@lumcon.edu
Id:https://orcid.org/0000-0002-3352-2564
Role:Funding Acquisition; Conceptualization; Supervision; Investigation; Methodology; Formal Analysis; Data curation
Individual: H Maurice Valett
Organization:University of Montana
Email Address:
Maury.Valett@mso.umt.edu
Id:https://orcid.org/0000-0001-7146-6420
Role:Funding Acquisition; Conceptualization
Individual: Claire Utzman
Organization:University of Montana
Email Address:
claire.utzman@mso.umt.edu
Id:https://orcid.org/0000-0002-3228-8470
Role:Investigation
Individual: James R Junker
Organization:Michigan Technological University
Email Address:
jrjunker@mtu.edu
Id:https://orcid.org/0000-0001-9713-2330
Role:Formal Analysis; Data curation
Individual: Venice Bayrd
Organization:Montana State University
Email Address:
venice.bayrd@montana.edu
Id:https://orcid.org/0000-0002-5814-9380
Role:Data curation
Individual: Robert A Payn
Organization:Montana State University
Email Address:
rpayn@montana.edu
Id:https://orcid.org/0000-0001-8421-525X
Role:Funding Acquisition; Conceptualization; Data curation
Individual: Patrick Hurley
Organization:University of Montana
Email Address:
patrick.hurley@umontana.edu
Role:Investigation
Individual: Marc Peipoch
Organization:Stroud Water Research Center
Email Address:
mpeipoch@stroudcenter.org
Id:https://orcid.org/0000-0002-5943-831X
Role:Funding Acquisition; Conceptualization
Individual: Michael D DeGrandpre
Organization:University of Montana
Email Address:
michael.degrandpre@mso.umt.edu
Id:https://orcid.org/0000-0003-1969-6709
Role:Funding Acquisition; Conceptualization

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2017-08-15
End:
2018-09-27
Sampling Site: 
Description:Site ID 001, restoration project reach A: bridge on Garnet Way (site name: Warm Springs)
Site Coordinates:
Longitude (degree): -112.770111111111Latitude (degree): 46.1870222222222
Sampling Site: 
Description:Site ID 002, restoration project reach A: bridge on Perkins Rd from frontage access, location of Galen USGS gauge 12323800 (site name: Perkins)
Site Coordinates:
Longitude (degree): -112.767502777778Latitude (degree): 46.2084666666667
Sampling Site: 
Description:Site ID 003, restoration project reach A: bridge on Galen Road (site name: Galen)
Site Coordinates:
Longitude (degree): -112.753194444444Latitude (degree): 46.2373
Sampling Site: 
Description:Site ID 004, restoration project reach A: bridge on corner of W River Road and Gembeck Road, upstream of of Racetrack exit (site name: Racetrack)
Site Coordinates:
Longitude (degree): -112.744577777778Latitude (degree): 46.2654055555556
Sampling Site: 
Description:Site ID 005, restoration project reach A: bridge on Sager Lane (site name: Sager)
Site Coordinates:
Longitude (degree): -112.736238888889Latitude (degree): 46.3172666666667
Sampling Site: 
Description:Site ID 006, restoration project reach A: DL park on frontage Rd north of bridge, samples taken via (site name: Deer Lodge)
Site Coordinates:
Longitude (degree): -112.738411111111Latitude (degree): 46.3829861111111
Sampling Site: 
Description:Site ID 007, restoration project reach A: bridge on Rock Creek Cattle Rd (site name: Cattle Rd)
Site Coordinates:
Longitude (degree): -112.72825Latitude (degree): 46.4727722222222
Sampling Site: 
Description:Site ID 008, restoration project reach A: Above LBF River- river access from the fishing access road off the Beck Hill exit before the fishing loop from the road (site name: Garrison)
Site Coordinates:
Longitude (degree): -112.739544444444Latitude (degree): 46.4985388888889
Sampling Site: 
Description:Site ID 009, restoration project reach B: below bridge on Gold Cr road, access is downstream, river right (site name: Gold Creek)
Site Coordinates:
Longitude (degree): -112.928541666667Latitude (degree): 46.5901027777778
Sampling Site: 
Description:Site ID 010, restoration project reach B: Bear Mouth rest stop on I90 W, upstream end of parking lot, just downstream of lone pine on bank (site name: Bear Gulch)
Site Coordinates:
Longitude (degree): -113.345752777778Latitude (degree): 46.7037916666667
Sampling Site: 
Description:Site ID 011, restoration project reach B: Downstream from the bridge for Gillespie-Sliderock Road (site name: Bonita)
Site Coordinates:
Longitude (degree): -113.5724Latitude (degree): 46.7217694444444
Sampling Site: 
Description:Site ID 012, restoration project reach C: bridge on Turah Rd (site name: Turah)
Site Coordinates:
Longitude (degree): -113.813647222222Latitude (degree): 46.8262416666667
Sampling Site: 
Description:Site ID 013, restoration project reach Middle Fork: foot bridge on Madison, UM (site name: Missoula)
Site Coordinates:
Longitude (degree): -113.983116666667Latitude (degree): 46.8674388888889

Project

Parent Project Information:

Title:LTREB: Collaborative research - River ecosystem responses to floodplain restoration
Personnel:
Individual: H Maurice Valett
Organization:University of Montana
Email Address:
Maury.Valett@mso.umt.edu
Id:https://orcid.org/0000-0001-7146-6420
Role:Principal Investigator
Funding: US National Science Foundation 1655197
Related Project:
Title:LTREB: Collaborative research - River ecosystem responses to floodplain restoration
Personnel:
Individual: Robert A Payn
Organization:Montana State University
Email Address:
rpayn@montana.edu
Id:https://orcid.org/0000-0001-8421-525X
Role:Principal Investigator
Funding: US National Science Foundation 1655198
Related Project:
Title:RII Track-1 Consortium for Research on Environmental Water Systems
Personnel:
Individual: Ragan M Callaway
Organization:University of Montana
Email Address:
Ray.Callaway@mso.umt.edu
Id:https://orcid.org/0000-0001-7342-4312
Role:Principal Investigator
Funding: US National Science Foundation OIA-1757351

Maintenance

Maintenance:
Description:Completed: Updates to these data are not expected
Frequency:
Other Metadata

Additional Metadata

additionalMetadata
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        |     |     |___element 'release'
        |     |     |     |___text '3.5.5'
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