Data Package Metadata View Summary

Characterization of pigments in photosynthetic benthic biomass on the river bed of the Upper Clark Fork River (Montana, USA) during the algal growing season of 2020

General Information

Data Package:

Local Identifier:

edi.1023.6

Title:

Characterization of pigments in photosynthetic benthic biomass on the river bed of the Upper Clark Fork River (Montana, USA) during the algal growing season of 2020

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 data in this product was to assess the response of the river algal community to the floodplain restoration. Data are measurements of benthic biomass organic matter standing stocks and pigments associated with primary producers. Benthic biomass data were collected on the UCFR (USGS HUC 17010201) at seven monitoring sites distributed from Warm Springs (near Anaconda, MT) to Bonita (east of Missoula, MT). Data from the Deer Lodge and Garrison sites were obtained from the River Algal Succession Study, a project funded by the Montana Consortium for Research on Environmental Water Systems. Data from Bonita were obtained from the Nitrogen Fixation Algal Study, a Research Experience for Undergraduates project. Benthic samples were obtained using a cylindrical benthic sampler isolating a known area of the river bed. Five samples were obtained at each site. Estimates of organic matter in biomass were obtained from area-normalized ash-free dry mass. Algal pigment concentrations for chlorophyll and phaeophytin were obtained through the use of extraction in acetone followed by spectroscopy. Phycocyanin concentrations were measured in aqueous suspension (in-vivo) with a fluorometer. Biomass compartments were discriminated between epilithon on river bed substrate, epiphyton on filamentous algae, terrestrial coarse particulate organic carbon, deposited fine benthic organic matter, and macrophytes. Data are from the 2020 algal growing season.

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.

Publication Date:

2023-04-22

For more information:
Visit:	DOI PLACE HOLDER

Time Period

Begin:

2020-07-13

End:

2020-10-20

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

Data Entities
Data Table Name:	Biomass_2020.csv
Description:	Analysis-ready characterization of organic matter and pigments in CPOM, epilithon, epiphyton, FBOM, filamentous algae, and macrophytes sampled from a known area of the river bed substrate at study sites along the Upper Clark Fork River
Other Name:	Biomass_2020_meta.csv
Description:	Metadata describing the content of columns in the associated data table (comma delimited tabular text file)
Other Name:	Biomass_2020_vis.pdf
Description:	Summary visualization of the riverbed biomass data included in this product (postscript data file).
Other Name:	0_Data.zip
Description:	Compressed data pipeline folder containing raw data files and project default metadata. See methods for details.
Other Name:	1_Protocol.zip
Description:	Compressed data pipeline folder containing R markdown and R scripts for processing data and metadata. See methods for details.
Other Name:	2_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


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1023/6/bbd313e90e1782647effe06c893e5521
Name:	Biomass_2020.csv
Description:	Analysis-ready characterization of organic matter and pigments in CPOM, epilithon, epiphyton, FBOM, filamentous algae, and macrophytes sampled from a known area of the river bed substrate at study sites along the Upper Clark Fork River
Number of Records:	285
Number of Columns:	53

Table Structure

Object Name:

Biomass_2020.csv

Size:

117283 bytes

Authentication:

36d51f460a73115cab6de4cf1a4ca144 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

DATE

SITE

SAMPLE

PROJECT

SUBSTRATE

AVERAGE_DEPTH

CPOM_OM_AREA_g_m2

CPOM_ASH_AREA_g_m2

EPIL_OM_AREA_g_m2

EPIL_ASH_AREA_g_m2

EPIL_CHLA_MG_M2_HAUER

EPIL_PHAEO_MG_M2_HAUER

EPIL_640_664

EPIL_PHICOCYANIN_MG_M2

EPIL_CHLA_MG_M2_RITCHIE

EPIL_CHLB_MG_M2_RITCHIE

EPIL_CHLC_MG_M2_RITCHIE

EPIL_CHLD_MG_M2_RITCHIE

EPIL_CHL_TOTAL_MG_M2_RITCHIE

EPIP_OM_AREA_g_m2

EPIP_ASH_AREA_g_m2

EPIP_CHLA_MG_M2_HAUER

EPIP_PHAEO_MG_M2_HAUER

EPIP_640_664

EPIP_PHICOCYANIN_MG_M2

EPIP_CHLA_MG_M2_RITCHIE

EPIP_CHLB_MG_M2_RITCHIE

EPIP_CHLC_MG_M2_RITCHIE

EPIP_CHLD_MG_M2_RITCHIE

EPIP_CHL_TOTAL_MG_M2_RITCHIE

FBOM_OM_AREA_g_m2

FBOM_ASH_AREA_g_m2

FBOM_CHLA_MG_M2_HAUER

FBOM_PHAEO_MG_M2_HAUER

FBOM_640_664

FBOM_PHICOCYANIN_MG_M2

FBOM_CHLA_MG_M2_RITCHIE

FBOM_CHLB_MG_M2_RITCHIE

FBOM_CHLC_MG_M2_RITCHIE

FBOM_CHLD_MG_M2_RITCHIE

FBOM_CHL_TOTAL_MG_M2_RITCHIE

FILA_OM_AREA_g_m2

FILA_ASH_AREA_g_m2

FILA_CHLA_MG_M2_HAUER

FILA_PHAEO_MG_M2_HAUER

FILA_640_664

FILA_CHLA_MG_M2_RITCHIE

FILA_CHLB_MG_M2_RITCHIE

FILA_CHLC_MG_M2_RITCHIE

FILA_CHLD_MG_M2_RITCHIE

FILA_CHL_TOTAL_MG_M2_RITCHIE

MACRO_OM_AREA_g_m2

MACRO_ASH_AREA_g_m2

Definition:

Summary: Date of sample collection using a Gregorian calendar in US Mountain time (America/Denver); Property: Time; Entity: Collection of a river water sample; Method: Field sample management protocol

Summary: Identifier for site location; Property: Location; Entity: Upper Clark Fork River geography; Method: Field sample management protocol

Summary: Identifier for replicate samples; Property: Replicate identifier; Entity: Sampling of river water; Method: Field sample management protocol

Summary: Identifier for the project motivating the data collection; Property: Primary project affiliation; Entity: Data record; Method: Field sample management protocol

Summary: Type of stream or river bed substrate; Property: Category of sediment size; Entity: Stream or river bed substrate; Method: Field sample management protocol

Summary: Average depth of water in the substrate sampler; Property: Average water depth; Entity: River water at substrate sampling locations; Method: Stage measurement

Summary: Areal density (mass per area) of terrestrial coarse particulate organic matter from the stream bed; Property: Areal density (mass per area) of organic matter; Entity: Terrestrial coarse particulate organic matter from top surface of sampled stream bed substrate; Method: Ashing and reweighing of a sample from a measured surface area of substrate

Summary: Areal density (mass per area) of ash remaining after combustion of stream bed terrestrial coarse particulate organic matter; Property: Areal density (mass per area) of ash remaining after combustion; Entity: Terrestrial coarse particulate organic matter from top surface of sampled stream bed substrate; Method: Ashing and reweighing of a sample from a measured surface area of substrate

Summary: Areal density (mass per area) of organic matter in stream bed epilithon; Property: Areal density (mass per area) of organic matter; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Ashing and reweighing of residue after filtering a sample from a measured surface area of substrate

Summary: Areal density (mass per area) of ash remaining after combustion of stream bed epilithic material; Property: Areal density (mass per area) of ash remaining after combustion; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Ashing and reweighing of residue after filtering a sample from a measured surface area of substrate

Summary: Areal density of chlorophyll a in stream bed epilithon; Property: Areal density (mass per area) of chlorophyll a; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate

Summary: Areal density (mass per area) of phaeophytin in stream bed epilithon; Property: Areal density (mass per area) of phaeophytin; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate

Summary: Carotenoid to chlorophyll ratio in stream bed epilithon; Property: Carotenoid to chlorophyll ratio; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate

Summary: Areal density (mass per area) of phycocyanin in stream bed epilithon; Property: Areal density (mass per area) of phycocyanin; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Fluorometric measurement of an in vivo sample from a measured surface area of substrate

Summary: Areal density of chlorophyll b in stream bed epilithon; Property: Areal density (mass per area) of chlorophyll b; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density of chlorophyll c in stream bed epilithon; Property: Areal density (mass per area) of chlorophyll c; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density of chlorophyll d in stream bed epilithon; Property: Areal density (mass per area) of chlorophyll d; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density of total chlorophyll in stream bed epilithon; Property: Areal density (mass per area) of total chlorophyll; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density (mass per area) of organic matter in stream bed epiphyton; Property: Areal density (mass per area) of organic matter; Entity: Epiphyton from surface of filamentous algae sampled stream bed substrate; Method: Ashing and reweighing of residue after filtering a sample from a measured surface area of substrate

Summary: Areal density (mass per area) of ash remaining after combustion of stream bed epiphyton material; Property: Areal density (mass per area) of ash remaining after combustion; Entity: Epiphyton from surface of filamentous algae sampled stream bed substrate; Method: Ashing and reweighing of residue after filtering a sample from a measured surface area of substrate

Summary: Areal density of chlorophyll a in stream bed epiphyton; Property: Areal density (mass per area) of chlorophyll a; Entity: Epiphyton from surface of filamentous algae sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate

Summary: Areal density (mass per area) of phaeophytin in stream bed epiphyton; Property: Areal density (mass per area) of phaeophytin; Entity: Epiphyton from surface of filamentous algae sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate

Summary: Carotenoid to chlorophyll ratio in stream bed epiphyton; Property: Carotenoid to chlorophyll ratio; Entity: Epiphyton from surface of filamentous algae sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate

Summary: Areal density (mass per area) of phycocyanin in stream bed epiphyton; Property: Areal density (mass per area) of phycocyanin; Entity: Epiphyton from surface of filamentous algae sampled stream bed substrate; Method: Fluorometric measurement of an in vivo sample from a measured surface area of substrate

Summary: Areal density of chlorophyll b in stream bed epiphyton; Property: Areal density (mass per area) of chlorophyll b; Entity: Epiphyton from surface of filamentous algae sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density of chlorophyll c in stream bed epiphyton; Property: Areal density (mass per area) of chlorophyll c; Entity: Epiphyton from surface of filamentous algae sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density of chlorophyll d in stream bed epiphyton; Property: Areal density (mass per area) of chlorophyll d; Entity: Epiphyton from surface of filamentous algae sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density of total chlorophyll in stream bed epiphyton; Property: Areal density (mass per area) of total chlorophyll; Entity: Epiphyton from surface of filamentous algae sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density (mass per area) of fine benthic organic matter on the stream bed; Property: Areal density (mass per area) of organic matter; Entity: Fine benthic organic matter from top surface of sampled stream bed substrate; Method: Ashing and reweighing of residue after filtering agitated water from a sampler with known area

Summary: Areal density (mass per area) of ash remaining after combustion of stream bed fine deposition material; Property: Areal density (mass per area) of ash remaining after combustion; Entity: Fine deposition material from top surface of sampled stream bed substrate; Method: Ashing and reweighing of residue after filtering agitated water from a sampler with known area

Summary: Areal density of chlorophyll a in stream bed fine benthic organic matter; Property: Areal density (mass per area) of chlorophyll a; Entity: Fine benthic organic matter from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a known surface area of substrate

Summary: Areal density (mass per area) of phaeophytin in stream bed fine benthic organic matter; Property: Areal density (mass per area) of phaeophytin; Entity: Fine benthic organic matter from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate

Summary: Carotenoid to chlorophyll ratio in stream bed fine benthic organic matter; Property: Carotenoid to chlorophyll ratio; Entity: Fine benthic organic matter from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate

Summary: Areal density (mass per area) of phycocyanin in stream bed fine benthic organic matter; Property: Areal density (mass per area) of phycocyanin; Entity: Fine benthic organic matter from top surface of sampled stream bed substrate; Method: Fluorometric measurement of an in vivo sample from a measured surface area of substrate

Summary: Areal density of chlorophyll b in stream bed fine benthic organic matter; Property: Areal density (mass per area) of chlorophyll b; Entity: Fine benthic organic matter from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density of chlorophyll c in stream bed fine benthic organic matter; Property: Areal density (mass per area) of chlorophyll c; Entity: Fine benthic organic matter from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density of chlorophyll d in stream bed fine benthic organic matter; Property: Areal density (mass per area) of chlorophyll d; Entity: Fine benthic organic matter from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density of total chlorophyll in stream bed fine benthic organic matter; Property: Areal density (mass per area) of total chlorophyll; Entity: Fine benthic organic matter from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density (mass per area) of organic matter in filamentous algae on the stream bed; Property: Areal density (mass per area) of organic matter; Entity: Filamentous algae from top surface of sampled stream bed substrate; Method: Ashing and reweighing of a sample from a measured surface area of substrate

Summary: Areal density (mass per area) of ash remaining after combustion of stream bed filamentous algal material; Property: Areal density (mass per area) of ash remaining after combustion; Entity: Filamentous algal material from top surface of sampled stream bed substrate; Method: Ashing and reweighing of a sample from a measured surface area of substrate

Summary: Areal density of chlorophyll a in stream bed filamentous algae; Property: Areal density (mass per area) of chlorophyll a; Entity: Filamentous algae from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate

Summary: Areal density (mass per area) of phaeophytin in stream bed filamentous algae; Property: Areal density (mass per area) of phaeophytin; Entity: Filamentous algae from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate

Summary: Carotenoid to chlorophyll ratio in stream bed filamentous algae; Property: Carotenoid to chlorophyll ratio; Entity: Filamentous benthic algae from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate

Summary: Areal density of chlorophyll b in stream bed filamentous algae; Property: Areal density (mass per area) of chlorophyll b; Entity: Filamentous algae from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density of chlorophyll c in stream bed filamentous algae; Property: Areal density (mass per area) of chlorophyll c; Entity: Filamentous algae from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density of chlorophyll d in stream bed filamentous algae; Property: Areal density (mass per area) of chlorophyll d; Entity: Filamentous algae from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density of total chlorophyll in stream bed filamentous algae; Property: Areal density (mass per area) of total chlorophyll; Entity: Filamentous algae from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)

Summary: Areal density (mass per area) of organic matter in macrophytes on the stream bed; Property: Areal density (mass per area) of organic matter; Entity: Macrophytes from top surface of sampled stream bed substrate; Method: Ashing and reweighing of a sample from a measured surface area of substrate

Summary: Areal density (mass per area) of ash remaining after combustion of stream bed macrophytes; Property: Areal density (mass per area) of ash remaining after combustion; Entity: Macrophytes from top surface of sampled stream bed substrate; Method: Ashing and reweighing of a sample from a measured surface area of substrate

Storage Type:

date

string

float

Measurement Type:

dateTime

nominal

ratio

Measurement Values Domain:

Format	YYYYMMDD
Precision

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	001
Definition	Project site number 001
Source

Code Definition

Code	006
Definition	Project site number 006
Source

Code Definition

Code	007
Definition	Project site number 007
Source

Code Definition

Code	008
Definition	Project site number 008
Source

Code Definition

Code	009
Definition	Project site number 009
Source

Code Definition

Code	010
Definition	Project site number 010
Source

Code Definition

Code	011
Definition	Project site number 011
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1
Definition	Replicate sample 1
Source

Code Definition

Code	2
Definition	Replicate sample 2
Source

Code Definition

Code	3
Definition	Replicate sample 3
Source

Code Definition

Code	4
Definition	Replicate sample 4
Source

Code Definition

Code	5
Definition	Replicate sample 5
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	LTREB
Definition	LTREB core monitoring
Source

Code Definition

Code	RASS
Definition	RASS project from CREWS
Source

Code Definition

Code	NFAS
Definition	NFAS REU project from LTREB
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	COBBLE
Definition	Riverbed cobble substrate
Source

Code Definition

Code	PEBBLE
Definition	Riverbed pebble substrate
Source

Code Definition

Code	SAND
Definition	Riverbed sand substrate
Source

Unit	centimeter
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Max	55.75

Unit	gramsPerSquareMeter
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Unit	gramsPerSquareMeter
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Unit	dimensionless
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Unit	dimensionless
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Unit	milligramsPerSquareMeter
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Min	0
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Unit	gramsPerSquareMeter
Type	real
Min	0
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Unit	gramsPerSquareMeter
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Missing Value Code:

Code	NA
Expl	Missing value

Code	NA
Expl	Missing value

Code	NA
Expl	Missing value

Code	NA
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Code	NA
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Code	NA
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Code	NA
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Code	NA
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Code	NA
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Code	NA
Expl	Missing value

Code	NA
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Code	NA
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Code	NA
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Code	NA
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Coverage:

Methods:

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Data Package Usage Rights

Intellectual rights to the data of this data package are treated separately from those that apply 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 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. Files released under this license include those containing code in the following folders: Copyright 2023 - Rafael Feijó de Lima - *1\_protocol.zip/* - *2\_Calculation/* - *3\_Integration/* Copyright 2023 - Robert Payn - *1\_protocol.zip/* - *6\_metadata/* ### 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. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ## DATA RIGHTS STATEMENT The data selection and arrangement; documentation; metadata; and all data in this product not explicitly listed in the code license specified above are available under CC0 1.0 Universal Public Domain Dedication. The full Legal Code text is available below, and also here: https://creativecommons.org/publicdomain/zero/1.0/legalcode. ### Legal Code Text - CC0 1.0 Universal Public Domain Dedication Statement of Purpose The laws of most jurisdictions throughout the world automatically confer exclusive Copyright and Related Rights (defined below) upon the creator and subsequent owner(s) (each and all, an "owner") of an original work of authorship and/or a database (each, a "Work"). Certain owners wish to permanently relinquish those rights to a Work for the purpose of contributing to a commons of creative, cultural and scientific works ("Commons") that the public can reliably and without fear of later claims of infringement build upon, modify, incorporate in other works, reuse and redistribute as freely as possible in any form whatsoever and for any purposes, including without limitation commercial purposes. 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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, phycocyanin, epilithon, epiphyton
LTER Controlled Vocabulary	organic matter, algae, biomass, benthos, chlorophyll, phaeophytin, particulate 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:

## Measurement methods Where more details are available, each description below is cross-referenced with the brief methods caption provided in the descriptions of the columns in full metdata for Data Tables under the Data Entities heading. The detailed standards of practice for the collection of these data are available in 1\_Protocol.zip/SOP\_Biomass Samplng\_and\_Processing\_RFL\_08\_APR\_23.docx ### *Field sample management protocol* At each sampling site, 5 locations were chosen for sampling of benthic organic matter using a cylindrical sampler. Average water depth was first measured in the sampler. From the bed isolated by the sampler, organic matter was collected, including: coarse particulate organic matter; rocks with epilithon, filamentous algae, and associated epiphyton; macrophytes; and fine benthic organic matter suspended by agitation. After removal of filamentous algae, each rock was processed for epilithon by conventional scrubbing and rinsing from a measured surface area of the rock (Hauer and Lamberti 2017). All resulting samples were bagged in the field and kept in a dark cooler for transport to the lab, where they were stored at 4 degrees Celsius until analysis. ### *Stage measurement* Depth was measured with a meter stick at 4 cardinal locations around the edge of the cylindrical substrate sampler. ### *Ashing and reweighing of a sample from a measured surface area of substrate* Samples were dried, weighed, combusted in a furnace, and reweighed. Dry weight was the weight after drying. Ash weight was the weight after combustion. Organic matter weight was estimated as the difference between dry weight and ash weight (i.e., the ash-free dry mass or AFDM). This method applies to the CPOM and macrophyte sample processing (Hauer and Lamberti 2017). ### *Ashing and reweighing of residue after filtering a sample from a measured surface area of substrate* Organic matter standing stocks were obtained through a gravimetric approach based on residue from filtering a known volume of sample through a 0.7-micron GFF filter or a 1-2 gram subsample of a bulk sample of filamentous algal biomass collected from a measured surface area of the rock. The residue or subsample were dried until reaching a constant mass, combusted in a muffle furnace, and then reweighed to determine the mass of remaining ash. Ash-free dry mass of organic matter was determined by subtracting the mass of inorganic ash from the dry weight that includes combustible organic matter. This method applied to the epilithon and epiphyton samples (Hauer and Lamberti 2017). ### *Ashing and reweighing of residue after filtering agitated water from a sampler with known area* A sample of the fine benthic organic matter suspended in river water by agitation in the sampler was filtered on a pre-weighed filter. The filter and residue were dried, weighed, combusted in a furnace, and reweighed. Dry weight was the weight after drying. Ash weight was the weight after combustion. Organic matter weight was estimated as the difference between dry weight and ash weight (i.e., the ash-free dry mass or AFDM, Hauer and Lamberti 2017). ### *Spectrophotometric measurement of an extracted sample from a measured surface area of substrate* Pigment standing stocks in FBOM, epilithon, and epiphyton were obtained from the residue of filtering a known volume of sample onto a 0.7-micron GFF filter. Pigment standing stocks in filamentous algae were extracted from a 0.5-g sample of filaments. Pigments were extracted from samples for 24h in a 90% buffered acetone solution. Absorbance of light at specific wavelengths was measured pre- and post- acidification of extracts for turbidity-corrected chlorophyll a and phaeophytin quantification (664, 665, and 750nm). The ratio of carotenoids to chlorophyll a was estimated from the ratio of 640 nm to 664 nm absorbances (Hauer and Lamberti 2017). ### *Spectrophotometric measurement of an extracted sample from a measured surface area of substrate (Ritchie 2008)* Absorbances were also measured at three wavelengths (630, 647 and 691nm). Using these additional measurements, chlorophylls a-d and total chlorophyll were estimated using the quadrichroic equation (using absorbances at 630, 647, 665 and 691nm) described in Ritchie (2008). ### *Fluorometric measurement of an in vivo sample from a measured surface area of substrate* Phycocyanin concentrations were estimated in FBOM, epilithon, and epiphyton samples using a handheld fluorometer by measuring in-vivo concentrations prior to filtration. ## 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. Where available, raw data files from instruments and manufacturer software are available in the 0\_Data.zip file. The coding used to process the data is available in the 1\_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 2\_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 0\_Data.zip* - *meta/* - Directory with project templates for metadata - *attributes.xlsx* - Microsoft Excel file with commonly used table column attributes in the project - *people.xlsx* - Microsoft Excel file with tabular data on people associated with the project used for metadata generation. - *sites\_main.xlsx* - Microsoft Excel file with authoritative project site list at the time of publication of these data. ### *Contents of 1\_Protocol.zip* - *1\_Digitalization/* - Directory for digitalization protocol - *\*\_TEMPLATE\_DIG.xlsx* - Microsoft Excel templates for digitizing data from field sheets - *2\_Calculation/* - Directory with code for organic matter and pigment calculations for each biomass compartment - *CALC\_ALL.R* - R code that performs calculations for organic matter and pigments for each biomass compartment - *RASS\_SITENAMES.R* - R code for organizing RASS project data - *3\_Integration/* - Directory with code for integrating data tables - *INTEGRATION.R* - R code that integrates the calculated data into a single table - *4\_QAQC/* - Directory with quality assurance information - *READ ME!.txt* - Notes on QAQC - *5\_ISF\_Generation/* - Directory with information about final table generation - *ISF\_template\_20200813\_RFL.xlsx* - Template for final data tables - *6\_metadata/* - Directory with code for processing metadata and generating EML - *pkgs/* - Folder with locally installed R packages for customized features - *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 (2\_Incremental.zip/6\_metadata/processing\_notes.html) - *05\_ui\_narrative.R* - shiny R app for managing narrative metadata (requires external package) - *05\_ui\_people.R* - shiny R app for managing people metadata (requires external package) - *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 in the data product (readme.html) and an EML file (eml.xml). - R code in this folder depends on external R packages: knitr, readxl, rmarkdown, purrr, 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. - *Biomass Code Walkthrough Notes.docx* - Notes on protocol code execution - *RStudioProject.Rproj* - An RStudio project file provided for convenience in working with the code generating this data product with the appropriate working directory. - *SOP\_Biomass Samplng\_and\_Processing\_RFL\_08\_APR\_23.docx* - Standards of practice for sampling ### *Contents of 2\_Incremental.zip* - *1\_Digitalization/* - Directory for digitalization protocol - *\*\_DIG.xlsx* - Microsoft Excel digitalizations of the data sheets - *2\_Calculation/* - Directory with code for organic matter and pigment calculations for each biomass compartment - *\*.RESULT.csv* - Compiled results of calculations for each biomass compartment - *3\_Integration/* - Directory with code for integrating data tables - *INTEGRATED.csv* - An integrated table of data ready for quality checks - *5\_ISF\_Generation* - Directory with QAQC incremental data - *LTREB\_BIOMASS\_PIGMENTS\_2020\_ISF.csv* - Finalized data table - *LTREB\_BIOMASS\_PIGMENTS\_2020\_ISF\_QAQC.csv* - Incremental data table in the process of QAQC - *6\_metadata/* - Directory with incremental metadata - *LTREB\_BIOMASS\_PIGMENTS\_2020\_DICTIONARY.xlsx* - Original metadata for 2020 data (for reference only, not all entries verified) - *LTREB\_BIOMASS\_PIGMENTS\_2020\_EDI\_METADATA.docx* - Original metadata for 2020 data (for reference only, not all entries verified) - *metadata\_narrative.RData* - R data file with narrative metadata (created by Shiny R app) - *metadata\_people.RData* - R data file with people metadata (created by Shiny R app) - *processing\_notes.html* - Metadata regarding the processing of the raw data files to the product's data tables and basic visualizations. R code included in this product will generate temporary files in the ./2\_Incremental/.temp folder. These temporary files contain no unique data or metadata and thus are not archived in the corresponding zip file. ### *QAQC Notes* QAQC was performed following these criteria: 1. Some epilithon biomass values were likely wong. Main cause for error was probably poor drying of samples before ashing. Values were substituted by estimates based on the relationship between ashed mass and organic mass for all other samples, since that relationship was fairly constant. - y = 3.1639x + 12.4, R2 = 0.7227 - Specifically, rows: 27, 35, 48, 81, 131, 132, 133, 134, 135, 141, 142, 143, 144, 145 2. All values <0 were replaced with NAs, since negative values are not reasonable for any of the variables measured. 3. Outliers were not removed. Case by case analysis is advisable. ## References Hauer, F.R. and Lamberti, G. eds. 2017. Methods in stream ecology: Volume 1: Ecosystem structure. Academic Press. Ritchie, R. J. 2008. Universal chlorophyll equations for estimating chlorophylls a, b, c, and d and total chlorophylls in natural assemblages of photosynthetic organisms using acetone, methanol, or ethanol solvents. Photosynthetica 46: 115-126. [doi:10.1007/s11099-008-0019-7]. ## Data product development history - 2022 July 29: Original draft - Inquiry regarding Jens Bridge site ID - 2023 March 7 - Fixed Jens Bridge site info - Updated current practice on readme file and using CRediT taxonomy on personnel - 2023 April 2 - Addressing feedback from Rafa

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:

Rafael Feijó de Lima

Organization:

University of Montana

Email Address:

rafael.feijo@mso.umt.edu

Id:

https://orcid.org/0000-0001-8514-2195

Individual:

Claire Utzman

Organization:

University of Montana

Email Address:

claire.utzman@mso.umt.edu

Id:

https://orcid.org/0000-0002-3228-8470

Individual:

H Maurice Valett

Organization:

University of Montana

Email Address:

Maury.Valett@mso.umt.edu

Id:

https://orcid.org/0000-0001-7146-6420

Contacts:

Individual:

H Maurice Valett

Organization:

University of Montana

Email Address:

Maury.Valett@mso.umt.edu

Id:

https://orcid.org/0000-0001-7146-6420

Associated Parties:

Individual:

Rafael Feijó de Lima

Organization:

University of Montana

Email Address:

rafael.feijo@mso.umt.edu

Id:

https://orcid.org/0000-0001-8514-2195

Role:

Conceptualization; Investigation; Methodology; Formal Analysis; Data curation

Individual:

Claire Utzman

Organization:

University of Montana

Email Address:

claire.utzman@mso.umt.edu

Id:

https://orcid.org/0000-0002-3228-8470

Role:

Investigation; 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; Supervision

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:

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

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:

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

Temporal, Geographic and Taxonomic Coverage

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

Time Period

Begin:

2020-07-13

End:

2020-10-20

Sampling Site:

Description:

Site ID: 001; Common site name: Warm Springs; Restoration project reach: A; Description: bridge on Garnet Way

Site Coordinates:

Longitude (degree):

-112.770111111111

Latitude (degree):

46.1870222222222

Sampling Site:

Description:

Site ID: 006; Common site name: Deer Lodge; Restoration project reach: A; Description: DL park on frontage Rd north of bridge

Site Coordinates:

Longitude (degree):

-112.738411111111

Latitude (degree):

46.3829861111111

Sampling Site:

Description:

Site ID: 007; Common site name: Cattle Rd; Restoration project reach: A; Description: bridge on Rock Creek Cattle Rd

Site Coordinates:

Longitude (degree):

-112.72825

Latitude (degree):

46.4727722222222

Sampling Site:

Description:

Site ID: 008; Common site name: Garrison; Restoration project reach: A; Description: Above LBf River- river access from the fishing access road off the Beck Hill exit before the fishing loop from the road

Site Coordinates:

Longitude (degree):

-112.739544444444

Latitude (degree):

46.4985388888889

Sampling Site:

Description:

Site ID: 009; Common site name: Gold Creek; Restoration project reach: B; Description: below bridge on Gold Cr road, access is downstream, river right

Site Coordinates:

Longitude (degree):

-112.928541666667

Latitude (degree):

46.5901027777778

Sampling Site:

Description:

Site ID: 010; Common site name: Bear Gulch; Restoration project reach: B; Description: Bear Mouth rest stop on I90 W, upstream end of parking lot, just downstream of lone pine on bank

Site Coordinates:

Longitude (degree):

-113.345752777778

Latitude (degree):

46.7037916666667

Sampling Site:

Description:

Site ID: 011; Common site name: Bonita; Restoration project reach: B; Description: Downstream from the bridge for Gillespie-Sliderock Road

Site Coordinates:

Longitude (degree):

-113.5724

Latitude (degree):

46.7217694444444

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
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'emlEditor'
        |     |     |___text '\n        '
        |     |     |___element 'app'
        |     |     |     |___text 'EMLassemblyline'
        |     |     |___text '\n        '
        |     |     |___element 'release'
        |     |     |     |___text '3.5.4'
        |     |     |___text '\n      '
        |     |___text '\n    '
        |___text '\n  '

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Data Package Metadata View Summary

Characterization of pigments in photosynthetic benthic biomass on the river bed of the Upper Clark Fork River (Montana, USA) during the algal growing season of 2020

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Data Table

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Data Package Usage Rights

Keywords

Methods and Protocols

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

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Parent Project Information:

Maintenance

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Data Package Metadata View Summary

Characterization of pigments in photosynthetic benthic biomass on the river bed of the Upper Clark Fork River (Montana, USA) during the algal growing season of 2020

+/- Data Entities

Data Table

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

+/- Data Package Usage Rights

+/- Keywords

+/- Methods and Protocols

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

+/- People and Organizations

+/- Temporal, Geographic and Taxonomic Coverage

+/- Project

Parent Project Information:

+/- Maintenance

+/- Additional Metadata

Data Entities

Data Package Usage Rights

Keywords

Methods and Protocols

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Maintenance

Additional Metadata