Data Package Metadata   View Summary

Laboratory reflectance spectra and pigments from giant kelp blades

General Information
Data Package:
Local Identifier:knb-lter-sbc.157.1
Title:Laboratory reflectance spectra and pigments from giant kelp blades
Alternate Identifier:DOI PLACE HOLDER
Abstract:

This dataset contains the whole blade reflectance and photosynthetic pigment concentrations from 1700 recently matured blades of giant kelp (Macrocystis pyrifera). The blades were collected at five sites along the California coast from 2012 to 2015.

Short Name:Kelp blade reflectance
Publication Date:2023-04-12
Language:English
For more information:
Visit: https://sbclter.msi.ucsb.edu/
Visit: DOI PLACE HOLDER

Time Period
Begin:
2012-08-07
End:
2015-08-06

People and Organizations
Contact:Information Manager, Santa Barbara Coastal LTER [  email ]
Organization:Santa Barbara Coastal LTER
Creator:Bell, Tom W 
Creator:Siegel, David A 

Data Entities
Data Table Name:
Blade reflectance
Description:
Blade reflectance
Data Table Name:
Blade pigments
Description:
Blade pigments
Other Name:
Blade reflectance and absorbance files
Description:
ZIP file containing text file outputs for each site
Other Name:
Matlab scripts
Description:
Matlab scripts
Detailed Metadata

Data Entities


Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-sbc/157/1/0be088055818155a4c99cf5583f0e14a
Name:Blade reflectance
Description:Blade reflectance
Number of Records:798270
Number of Columns:7

Table Structure
Object Name:blade_reflectance_long.csv
Size:23157768 byte
Authentication:be3674c105649abcc88c4589ecf2366b Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited: no
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 SiteYearMonthdayBlade IDWavelengthReflectance
Column Name:Site  
Year  
Month  
day  
Blade  
Wavelength_nm  
Reflectance_percent  
Definition:Study siteSampling yearSampling monthSampling dayBlade IDWavelength (nm)Reflectance (%)
Storage Type:string  
integer  
string  
integer  
integer  
integer  
float  
Measurement Type:nominaldateTimedateTimedateTimenominalratioratio
Measurement Values Domain:
Definitionany text
FormatYYYY
Precision1
FormatMM
Precision1
FormatDD
Precision1
Definitionany text
Unitnanometer
Precision1
Typeinteger
Unitpercent
Precision1e-04
Typereal
Missing Value Code:              
Accuracy Report:              
Accuracy Assessment:              
Coverage:              
Methods:              

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-sbc/157/1/c1be31acb74ee5025576488fad4cba0d
Name:Blade pigments
Description:Blade pigments
Number of Records:1770
Number of Columns:9

Table Structure
Object Name:blade_pigments.csv
Size:62270 byte
Authentication:b920ea650a1ab1da71916dad79acd49f Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited: no
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 SiteYearMonthdayBlade IDDisc weightChlA_nmol_gChlC_nmol_gFX_nmol_g
Column Name:Site  
Year  
Month  
day  
Blade  
Weight_g  
ChlA_nmol_g  
ChlC_nmol_g  
FX_nmol_g  
Definition:Study siteSampling yearSampling monthSampling dayBlade IDDisc weightConcentration of Chl a (nmol per g)Concentration of Chl c (nmol per g)fucoxanthin pigments (nmol per g)
Storage Type:string  
integer  
string  
integer  
integer  
float  
integer  
integer  
integer  
Measurement Type:nominaldateTimedateTimedateTimenominalratioratioratioratio
Measurement Values Domain:
Definitionany text
FormatYYYY
Precision1
FormatMM
Precision1
FormatDD
Precision1
Definitionany text
Unitgram
Precision0.001
Typereal
UnitnanomolesPerGram
Precision1
Typeinteger
UnitnanomolesPerGram
Precision1
Typeinteger
UnitnanomolesPerGram
Precision1
Typeinteger
Missing Value Code:                  
Accuracy Report:                  
Accuracy Assessment:                  
Coverage:                  
Methods:                  

Non-Categorized Data Resource

Name:Blade reflectance and absorbance files
Entity Type:otherEntity
Description:ZIP file containing text file outputs for each site
Physical Structure Description:
Object Name:Pigments.zip
Size:21914658 byte
Authentication:d6a5b95ed60eb256f45228315917b7e8 Calculated By MD5
Externally Defined Format:
Format Name:ZIP
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-sbc/157/1/54624816aa136c458f40ab879dba7a3c

Non-Categorized Data Resource

Name:Matlab scripts
Entity Type:otherEntity
Description:Matlab scripts
Physical Structure Description:
Object Name:Refl_Script.m
Size:5038 byte
Authentication:b7b1663bbeed36ba5ba569d4f53ee56a Calculated By MD5
Externally Defined Format:
Format Name:MATLAB
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-sbc/157/1/7542f094a7eafc499037d1e9c8570ec5

Data Package Usage Rights

This data package is released under the Creative Commons License Attribution 4.0 International (CC BY 4.0, see https://creativecommons.org/licenses/by/4.0/). This license states that consumers ("Data Users" herein) may distribute, adapt, reuse, remix, and build upon this work, as long as they give appropriate credit, provide a link to the license, and indicate if changes were made. If redistributed, a Data User may not apply additional restrictions or technological measures that prevent access.

The Data User has an ethical obligation to cite the data source appropriately in any publication or product that results from its use, and notify the data contact or creator. Communication, collaboration, or co-authorship (as appropriate) with the creators of this data package is encouraged to prevent duplicate research or publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplication or inappropriate use. The Data User should realize that misinterpretation may occur if data are used outside of the context of the original study. The Data User should be aware that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data.

While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. This data package (with 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 repository where these data were obtained shall not be liable for any damages resulting from misinterpretation, use or misuse of the data package or its components.

Keywords

By Thesaurus:
SBC-LTER Controlled VocabularyKelp Forest
Santa Barbara Coastal LTER PlacesSanta Cruz Island
Global Change Master Directory (GCMD) v6.0.0.0.0Pigments
noneMacrocystis pyrifera (Giant kelp), Santa Barbara Channel

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:

Field samples of giant kelp canopy blade reflectance and chlorophyll a, chlorophyll c, and fucoxanthin pigment concentration were taken at five kelp forest sites along the California coast: Arroyo Burro, Arroyo Quemado, and Mohawk kelp forests in the Santa Barbara Channel, La Jolla kelp forest near San Diego, and Pleasure Point kelp forest near Santa Cruz. Sites in the Santa Barbara Channel were sampled monthly over a three-year period (August 2012 – August 2015) and the La Jolla and Pleasure Point sites were sampled quarterly (May 2013 to July 2015). One mature blade (approximately 14 days of age) was collected 2 meters back from the tip of an actively growing frond from 15 different plants at each site. Blades were placed in a sealed plastic bag which was immediately placed on ice in an opaque cooler. The blades were then transported to the lab where they were stored at 4°C until being processed within 24 hours of collection.

A 5 cm square was cut from the center of each blade approximately 5 cm above the pneumatocyst and any epibionts were removed (blades usually had no epibionts). The reflectance of the square was then measured between 350 – 800 nm, at 1 nm intervals, using a Shimadzu UV 2401PC spectrophotometer with an integrating sphere attachment. Pigment concentration was determined from a 0.8 cm2 disc excised from the center of each square. Each disc was weighed and placed in 4 mL of dimethyl sulfoxide for 45 minutes at room temperature in the dark. The disc was then removed and washed with 1 mL water, bringing the total volume of the first extraction to 5 mL, before being placed in 5 mL of a 3:1:1 acetone, methanol, and water solution for 2 hours at 4°C in the dark. The extractions were placed in individual quartz cuvettes and absorbance was measured between 350 – 800 nm using the spectrophotometer. Pigment concentrations were determined using known absorbance-based equations (Seely et al. 1972).

References:

Bell, T.W., Cavanaugh, K.C., Siegel, D.A. (2015) Remote monitoring of giant kelp biomass and photosynthetic condition: An evaluation of the potential for the Hyperspectral Infrared Imager (HyspIRI) mission. Remote Sensing of Environment, 167, 218-228.

Bell, T.W., Reed, D.C., Nelson, N.B., Siegel, D. A. (2018), Regional patterns of physiological condition determine giant kelp primary production dynamics. Limnology and Oceanography, 63, 472-483.

Bell, T.W., Nidzieko, N., Siegel, D.A., Miller, R., Cavanaugh, Ky., Nelson, N., Reed, D., Federov, D., Cavanaugh, Ka., Moran, C., Snyder, J., Griffith, M. (2020), The utility of satellites and autonomous remote sensing platforms for monitoring offshore aquaculture farms: A case study for canopy forming kelps. Frontiers in Marine Science, 7:520223. 

Bell, T.W., Siegel, D.A. (2022), Nutrient availability and senescence spatially structure the dynamics of a foundation species, Proceedings of the National Academy of Sciences, 119, 1, e2105135118.

Seely, G., Duncan, M., Vidaver, W. (1972) Preparative and analytical extraction of pigments from brown algae with dimethyl sulfoxide. Mar. Biol. 188.

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@edirepository.org
Web Address:
https://edirepository.org
Id:https://ror.org/0330j0z60
Creators:
Organization:Santa Barbara Coastal LTER
Address:
Marine Science Institute University of California,
Santa Barbara, CA 93106 USA
Email Address:
sbclter@msi.ucsb.edu
Individual: Tom W Bell
Address:
Woods Hole Oceanographic Institution 266 Woods Hole Road,
Woods Hole, MA 02543 US
Email Address:
tbell@whoi.edu
Id:https://orcid.org/0000-0002-0173-2866
Individual: David A Siegel
Address:
Earth Research Institute University of California,
Santa Barbara, CA 93106-3060 US
Phone:
805-893-4547
Email Address:
davesiegel@ucsb.edu
Id:https://orcid.org/0000-0003-1674-3055
Contacts:
Position:Information Manager, Santa Barbara Coastal LTER
Address:
Marine Science Institute,
University of California,
Santa Barbara, California 93106-6150 United States
Phone:
805 893 2071 (voice)
Email Address:
sbclter@msi.ucsb.edu
Web Address:
https://sbclter.msi.ucsb.edu/

Temporal, Geographic and Taxonomic Coverage

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

Time Period
Begin:
2012-08-07
End:
2015-08-06
Sampling Site: 
Description:ABUR: Arroyo Burro Reef is located on the Santa Barbara Channel near the mouth of Arroyo Burro Creek and Beach. Depth ranges from 5.4 to 7 meters.
Site Coordinates:
Longitude (degree): -119.7445915Latitude (degree): 34.400275
Sampling Site: 
Description:AQUE: Arroyo Quemado Reef: Arroyo Quemado Reef depth range from 5.4 m to 10.7 m. Reference on Land is close to US101/Arroyo Quemada Ln.
Site Coordinates:
Longitude (degree): -120.11905Latitude (degree): 34.46774988
Sampling Site: 
Description:MOHK: Mohawk Reef: Mohawk Reef depth ranges from 4.5m to 6.0 m. Reference on land is Mohawk Rd / Edgewater Way.
Site Coordinates:
Longitude (degree): -119.72957Latitude (degree): 34.3940708
Sampling Site: 
Description:LJOA: La Jolla kelp forest near San Diego
Site Coordinates:
Longitude (degree): -117.277160Latitude (degree): 32.8542570
Sampling Site: 
Description:PLPT: Pleasure Point kelp forest near Santa Cruz
Site Coordinates:
Longitude (degree): -121.9631570Latitude (degree): 36.9581390

Project

Parent Project Information:

Title:Santa Barbara Coastal Long Term Ecological Research Project
Personnel:
Individual:Dr. Robert Miller
Address:
Marine Science Institute,
University of California,
Santa Barbara, California 93106-6150 United States
Phone:
805 893 6174 (voice)
Email Address:
miller@msi.ucsb.edu
Role:Principal Investigator
Individual:Dr. Dan Reed
Address:
Marine Science Institute,
University of California,
Santa Barbara, California 93106-6150 United States
Phone:
805 893 8363 (voice)
Email Address:
dan.reed@lifesci.ucsb.edu
Role:Co-principal Investigator
Individual:Dr. Adrian Stier
Address:
Department of Ecology, Evolution and Marine Biology,
University of California,
Santa Barbara, California 93106-9260 United States
Phone:
805 893 5467 (voice)
Email Address:
adrian.stier@lifesci.ucsb.edu
Role:Co-principal Investigator
Individual:Dr. Gretchen Hoffman
Address:
Department of Ecology, Evolution and Marine Biology,
University of California,
Santa Barbara, California 93106-9620 United States
Phone:
805 893 6175 (voice)
Email Address:
hofmann@lifesci.ucsb.edu
Role:Co-principal Investigator
Individual:Dr. David Siegel
Address:
Institute for Computational Earth System Science,
University of California,
Santa Barbara, California 93106-3060 United States
Phone:
805 893 4547 (voice)
Email Address:
davey@icess.ucsb.edu
Role:Co-principal Investigator
Abstract:

The Santa Barbara Coastal LTER (SBC LTER) is an interdisciplinary research and education program established in April 2000 with the goal of developing a predictive understanding of how environmental drivers interact with terrestrial and oceanic processes to alter material flows and influence the ecology of coastal ecosystems. SBC LTER's principal study domain is the semi-arid coast and nearshore waters of the Santa Barbara Channel in southern California, and its diverse and productive marine forests of giant kelp (Macrocystis pyrifera) serve as the focal study ecosystem. Analyses of our long-term data have identified many of the environmental drivers and ecological processes underlying the production and community dynamics of kelp forests. The research proposed to address this question is integrated in a conceptual framework that focuses on the causes and ecological consequences of the dynamics of a relatively short-lived foundation species in a setting of long-term climate change and human use.

Funding:

NSF Award OCE-9982105, OCE-0620276, OCE-1232779, OCE-1831937

Other Metadata

Additional Metadata

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