Green algae, cyanobacteria and diatom concentrations from the GCE-LTER Seawater Addition Long-Term Experiment (SALTEx) Project

Summary Information
Data Package General Information:
Local Identifier: knb-lter-gce.609.7
Title: Green algae, cyanobacteria and diatom concentrations from the GCE-LTER Seawater Addition Long-Term Experiment (SALTEx) Project
Alternate Identifier: ALG-GCED-1610.1.0
Alternate Identifier: doi:10.6073/pasta/cf4ee297faefab981268639685bca2ca
Abstract:

SALTEx (Seawater Addition Long-Term Experiment) is a field experiment designed to simulate saltwater intrusion in a tidal freshwater wetland to predict how chronic (Press) and acute (Pulse) salinization will affect this and other tidal freshwater ecosystems. The SALTEx experiment was initiated in 2012 and consists of 31 field plots , each 2.5 m on a side. There are three treatments (Press, Pulse, and Fresh) and two types of controls (with and without sides), each consisting of six replicates. The Press treatment plots receive regular (4 times each week) additions of a mixture of seawater and fresh river water. Pulse plots receive the same mixture of seawater and river water during September and October, which is historically a time of low flow in the river when natural saltwater intrusion occurs. The Fresh treatment plots receive regular additions of fresh river water. Treatment water is added during low tide to facilitate its infiltration into the soil, and all plots are inundated by astronomical tides at high tide. We are measuring the abundance of benthic algae with a BenthoTorch as one of the response variables for the SALTEx project.

Publication Date: 2017

Time Period
Begin:
2016-02-20
End:
2016-09-24

People and Organizations
Contact: GCE-LTER Information Manager [  email ]
Organization: Georgia Coastal Ecosystems LTER Project
Creator: Craft, Christopher B. (Indiana University at Bloomington)
Associate: Smith, Dontrece (University of Georgia Marine Institute)
Associate: Desha, Jennifer (University of Georgia Marine Institute)

Data Entities
Data Table Name:
ALG-GCED-1610
Description:
Main data table for data set ALG-GCED-1610
Other Name:
ALG-GCED-1610.kml
Description:
Google Earth Keyhole Markup Language file describing the geographic locations sampled in data set knb-lter-gce.609.7
Detailed Metadata

Data Entities


Data Table

Data: https://pasta.lternet.edu/package/data/eml/knb-lter-gce/609/7/2dfa38fdc9fb2666146758d1d65a1d08
Name: ALG-GCED-1610
Description: Main data table for data set ALG-GCED-1610
Number of Records: 992
Number of Columns: 11
Protocols and/or Procedures
Description:

Data file post-processing in the GCE-LTER Information Management Office

Software:
Title: GCE Data Toolbox for MATLAB(r)

Author(s):

Individual: Mr. Wade M. Sheldon
Address:
Dept. of Marine Sciences,
University of Georgia,
Athens, Georgia 30602-3636 USA
Email Address:
sheldon@uga.edu
Web Address:
http://gce-lter.marsci.uga.edu/public/app/personnel_bios.asp?id=wsheldon

Associated Parties:

Organization: Georgia Coastal Ecosystems LTER Project
Address:
Dept. of Marine Sciences,
University of Georgia,
Athens, Georgia 30602-3636 USA
Email Address:
gcelter@uga.edu
Role: sponsoring research program
Abstract:

The GCE Data Toolbox is a comprehensive library of functions for metadata-based analysis quality control, transformation and management of ecological data sets. The toolbox is based on the GCE Data Structure, a MATLAB specification for storing tabular data along with all information required to interpret the data and generate formatted metadata (documentation). Metadata fields in the structure are queried by toolbox functions for all operations, allowing functions to process and format values appropriately based on the type of information they represent. This semantic processing approach supports highly automated and intelligent data analysis and ensures data set validity throughout all processing steps.

Implementation Info:
Distribution:
Url: http://gce-lter.marsci.uga.edu/public/im/tools/toolbox_download.htm
Operating System: Linux
Operating System: Microsoft Windows
Operating System: Sun Solaris
Operating System: Apple Macintosh OS/X
Programming Language: MATLAB
Version Number: 3.x
Substep 1  
Description:

03/08/2017: new GCE Data Structure 1.1 created ("newstruct")

Substep 2  
Description:

03/08/2017: 992 rows imported from ASCII data file "ALG-GCED-1610.txt" ("imp_ascii")

Substep 3  
Description:

03/08/2017: 83 metadata fields in file header parsed ("parse_header")

Substep 4  
Description:

03/08/2017: data structure validated ("gce_valid")

Substep 5  
Description:

03/08/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 6  
Description:

03/08/2017: Name of column Mean_Elevation changed to Elevatio ("ui_editor")

Substep 7  
Description:

03/08/2017: updated 1 metadata fields in the Dataset sections ("addmeta")

Substep 8  
Description:

03/08/2017: imported Dataset, Project, Site, Study, Status, Supplement metadata descriptors from the GCE Metabase ("imp_gcemetadata")

Substep 9  
Description:

03/08/2017: updated 57 metadata fields in the Dataset, Project, Site, Status, Study, Supplement sections ("addmeta")

Substep 10  
Description:

03/28/2017: deleted column Date from the structure ("deletecols")

Substep 11  
Description:

03/28/2017: calculated calendar date in spreadsheet serial day (base 1/1/1900) format from individual date component columns Year, Month and Day, added "Date" column at position 4 ("add_datecol")

Substep 12  
Description:

03/28/2017: deleted column Date from the structure ("deletecols")

Substep 13  
Description:

03/28/2017: calculated calendar date in MM/DD/YYYY format from individual date component columns Year, Month and Day, added "Date" column at position 4 ("add_datecol")

Substep 14  
Description:

03/28/2017: updated 4 metadata fields ("addmeta")

Substep 15  
Description:

03/28/2017: updated 15 metadata fields in the Status, Data sections to reflect attribute metadata ("updatecols")

Substep 16  
Description:

03/28/2017: parsed and formatted metadata ("listmeta")

Quality Control
Quality Control Step 1:  
Description:

Quality control analysis was performed using the GCE Data Toolbox for MATLAB software. Column data types are validated upon importing the table into MATLAB, and qualifier flags are automatically generated for data values based on QA/QC criteria for each data column pre-defined in metadata templates (e.g. value range checks, sanity checks, pattern checks). Qualifier flags are also assigned to values that are imputed or derived, revised, or otherwise differ from values in the original data submission. A column of coded qualifier flags is generated and included in the data table if flags are assigned to any value in a data column.


Table Structure
Object Name: ALG-GCED-1610_1_0.CSV
Size: 52.37 kilobyte
Character Encoding: ASCII
Text Format:
Number of Header Lines: 5
Number of Foot Lines: 0
Record Delimiter: \r\n
Line Number For One Record: 1
Orientation: column
Simple Delimited:
Field Delimiter: ,
Quote Character: "

Table Column Descriptions
 
Column Name: Year  
Month  
Day  
Date  
Treatment  
Replicate  
Elevation  
Zone  
Green_algae_concentration  
Cyanobacteria_concentration  
Diatom_concentration  
Definition: Year the sample was collected Month the sample was collected Day the sample was collected Calendar date Sample treatment Replicate Mean elevation relative to MLW Zone of plot which was sampled Concentration of green algae as ug/cm2 Concentration of cyanobacteria as ug/cm2 Concentration of diatoms as ug/cm2
Storage Type: integer  
integer  
integer  
string  
string  
integer  
float  
integer  
float  
float  
float  
Measurement Type: interval interval interval dateTime nominal ordinal ratio ordinal ratio ratio ratio
Measurement Values Domain:
Unit nominalYear
Precision 1
Type whole
Min 2015 
Max 2016 
Unit nominalMonth
Precision 1
Type whole
Min
Max 12 
Unit nominalDay
Precision 1
Type whole
Min
Max 31 
Format MM/DD/YYYY
Precision 1
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code C
Definition Control
Source
Code Definition
Code CS
Definition Control w/ sides
Source
Code Definition
Code F
Definition Fresh
Source
Code Definition
Code PR
Definition Press
Source
Code Definition
Code PU
Definition Pulse
Source
Definition Replicate
Unit meter
Precision 0.00001
Type real
Definition Zone of plot which was sampled
Unit microgramsPerCentimeterSquared
Precision 0.01
Type real
Min
Max 1000 
Unit microgramsPerCentimeterSquared
Precision 0.01
Type real
Min
Max 1000 
Unit microgramsPerCentimeterSquared
Precision 0.01
Type real
Min
Max 1000 
Missing Value Code:
Code NaN
Expl value not recorded or censored based on quality control analysis (see methods)
Code NaN
Expl value not recorded or censored based on quality control analysis (see methods)
Code NaN
Expl value not recorded or censored based on quality control analysis (see methods)
   
Code NaN
Expl value not recorded or censored based on quality control analysis (see methods)
Code NaN
Expl value not recorded or censored based on quality control analysis (see methods)
Code NaN
Expl value not recorded or censored based on quality control analysis (see methods)
Code NaN
Expl value not recorded or censored based on quality control analysis (see methods)
Code NaN
Expl value not recorded or censored based on quality control analysis (see methods)
Code NaN
Expl value not recorded or censored based on quality control analysis (see methods)
Accuracy Report:                      
Accuracy Assessment:                      
Coverage:                      
Methods:                      

Non-Categorized Data Resource

Name: ALG-GCED-1610.kml
Entity Type: KML
Description: Google Earth Keyhole Markup Language file describing the geographic locations sampled in data set knb-lter-gce.609.7
Physical Structure Description:
Object Name: ALG-GCED-1610.kml
Externally Defined Format:
Format Name: application/vnd.google-earth.kml+xml
Data: https://pasta.lternet.edu/package/data/eml/knb-lter-gce/609/7/795cd1924c10893da2021879b13efd45

Data Package Usage Rights

This information is licensed under a Creative Commons Attribution 4.0 International License (see: https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) has an ethical obligation to cite it appropriately in any publication that results from its use. 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 duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data.

Keywords

By Thesaurus:
GCE-LTER Controlled Vocabulary Georgia, Sapelo Island, USA, Bentho Torch, cyanobacteria, GCE, Georgia Coastal Ecosystems, LTER, seawater intrusion
LTER Controlled Vocabulary algae, diatoms
LTER Core Research Areas Disturbance Patterns, Primary Production

Methods and Protocols

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

Protocols and/or Procedures
Description:

Bentho Sampling

Measuring chlorophyll, diatom, and cyanobacteria levels as well as reflectivity, and GPS location using the Bentho Torch.

Protocol:
Author: Craft
Title: SALTEx - BBE BenthoTorch Operational Protocol
Url: http://gce-lter.marsci.uga.edu/public/app/resource_details.asp?id=775
Protocol:
Author: Craft
Title: SALTEx - Bentho Torch Sampling Protocol
Url: http://gce-lter.marsci.uga.edu/public/app/resource_details.asp?id=777
Protocol:
Author: Widney
Title: SALTEx Map Plot Layout
Url: http://gce-lter.marsci.uga.edu/public/app/resource_details.asp?id=814
Instrument(s): Pennings Bentho Torch; manufacturer: bbe Moldaenke BmbH (model: Bentho Torch); parameter: algal concentration (accuracy: 0.1 µg chl-a/cm2, range: 0 - 15 µg chl-a/cm2)
Sampling Area and Study Extent
Sampling Description:

Bentho Torch

SALTEx was initiated in 2012 (measurements began in 2014) and consists of 31 field plots , each 2.5 m on a side. There are three treatments (Press, Pulse, and Fresh) and two types of controls (with and without sides), each consisting of six replicates. The replicates are blocked by elevation in statistical analyses. The Press treatment plots receive regular (4 times each week) additions of a mixture of seawater and fresh river water. Pulse plots receive the same mixture of seawater and river water during September and October, which is historically a time of low flow in the river when saltwater intrusion naturally occurs. The Fresh treatment plots receive regular additions of fresh river water. Response measurements include porewater chemistry, specifically concentrations of chloride, sulfate, sulfide, dissolved organic carbon (DOC), ammonium-N, nitrate/nitrite-N, dissolved reactive P, total P, total N, organic N, C:N ratio, org-C:org-N ratio, and pH. We are measuring the abundance of benthic algae (green algae, cyanobacteria, and diatoms) with a BenthoTorch as one of the response variables for the SALTEx project. We predict that abundance of benthic algae will increase in the Press plots as plants die due to the seawater additions.

The soil surface is non-destructively sampled for algae abundance using the BenthoTorch once every month. Every plot is sampled 4 times, one sampling each in zones 1, 3, 7, and 9. The specific area (1 cm2) sampled within each zone is different each month. The concentration of each type of benthic algae is calculated by the BenthoTorch and recorded by the field technician. The field technician then transfers the data to an Excel file.

Sampling Extent:

Time Period
Begin:
2016-02-20
End:
2016-09-24
Sampling Extent:
Geographic Region:
Description: GCE Study Site SALTEx -- SALTEx Research Site, Champney Island, Georgia, USA. SALTEX (Seawater Addition Long Term Experiment) is a long-term field experiment initiated by GCE-LTER in 2011 in a Zizaniopsis marsh along the Altamaha River. Due to the unprecedented spatial and temporal scale of this experiment, we anticipate that it will generate new insights into how low-salinity tidal marshes respond to saltwater intrusion. We are increasing porewater salinity in replicated plots from the ambient salinity of <0.5 to a target range of 5–8 in press treatments to simulate sea level rise and episodic (pulse) treatments with salinities elevated temporarily to simulate drought. See the project description at http://gce-lter.marsci.uga.edu/public/app/send_project_eml.asp?id=73 for more information.
Bounding Coordinates:
Northern:   31.339834 Southern:   31.338952
Western:   -81.467197 Eastern:   -81.466189

These methods, instrumentation, and/or protocols apply to the data table ALG-GCED-1610:

Protocols and/or Procedures
Description:

Data file post-processing in the GCE-LTER Information Management Office

Software:
Title: GCE Data Toolbox for MATLAB(r)

Author(s):

Individual: Mr. Wade M. Sheldon
Address:
Dept. of Marine Sciences,
University of Georgia,
Athens, Georgia 30602-3636 USA
Email Address:
sheldon@uga.edu
Web Address:
http://gce-lter.marsci.uga.edu/public/app/personnel_bios.asp?id=wsheldon

Associated Parties:

Organization: Georgia Coastal Ecosystems LTER Project
Address:
Dept. of Marine Sciences,
University of Georgia,
Athens, Georgia 30602-3636 USA
Email Address:
gcelter@uga.edu
Role: sponsoring research program
Abstract:

The GCE Data Toolbox is a comprehensive library of functions for metadata-based analysis quality control, transformation and management of ecological data sets. The toolbox is based on the GCE Data Structure, a MATLAB specification for storing tabular data along with all information required to interpret the data and generate formatted metadata (documentation). Metadata fields in the structure are queried by toolbox functions for all operations, allowing functions to process and format values appropriately based on the type of information they represent. This semantic processing approach supports highly automated and intelligent data analysis and ensures data set validity throughout all processing steps.

Implementation Info:
Distribution:
Url: http://gce-lter.marsci.uga.edu/public/im/tools/toolbox_download.htm
Operating System: Linux
Operating System: Microsoft Windows
Operating System: Sun Solaris
Operating System: Apple Macintosh OS/X
Programming Language: MATLAB
Version Number: 3.x
Substep 1  
Description:

03/08/2017: new GCE Data Structure 1.1 created ("newstruct")

Substep 2  
Description:

03/08/2017: 992 rows imported from ASCII data file "ALG-GCED-1610.txt" ("imp_ascii")

Substep 3  
Description:

03/08/2017: 83 metadata fields in file header parsed ("parse_header")

Substep 4  
Description:

03/08/2017: data structure validated ("gce_valid")

Substep 5  
Description:

03/08/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 6  
Description:

03/08/2017: Name of column Mean_Elevation changed to Elevatio ("ui_editor")

Substep 7  
Description:

03/08/2017: updated 1 metadata fields in the Dataset sections ("addmeta")

Substep 8  
Description:

03/08/2017: imported Dataset, Project, Site, Study, Status, Supplement metadata descriptors from the GCE Metabase ("imp_gcemetadata")

Substep 9  
Description:

03/08/2017: updated 57 metadata fields in the Dataset, Project, Site, Status, Study, Supplement sections ("addmeta")

Substep 10  
Description:

03/28/2017: deleted column Date from the structure ("deletecols")

Substep 11  
Description:

03/28/2017: calculated calendar date in spreadsheet serial day (base 1/1/1900) format from individual date component columns Year, Month and Day, added "Date" column at position 4 ("add_datecol")

Substep 12  
Description:

03/28/2017: deleted column Date from the structure ("deletecols")

Substep 13  
Description:

03/28/2017: calculated calendar date in MM/DD/YYYY format from individual date component columns Year, Month and Day, added "Date" column at position 4 ("add_datecol")

Substep 14  
Description:

03/28/2017: updated 4 metadata fields ("addmeta")

Substep 15  
Description:

03/28/2017: updated 15 metadata fields in the Status, Data sections to reflect attribute metadata ("updatecols")

Substep 16  
Description:

03/28/2017: parsed and formatted metadata ("listmeta")

Quality Control
Quality Control Step 1:  
Description:

Quality control analysis was performed using the GCE Data Toolbox for MATLAB software. Column data types are validated upon importing the table into MATLAB, and qualifier flags are automatically generated for data values based on QA/QC criteria for each data column pre-defined in metadata templates (e.g. value range checks, sanity checks, pattern checks). Qualifier flags are also assigned to values that are imputed or derived, revised, or otherwise differ from values in the original data submission. A column of coded qualifier flags is generated and included in the data table if flags are assigned to any value in a data column.

People and Organizations

Publishers:
Organization: Georgia Coastal Ecosystems LTER Project
Address:
Dept. of Marine Sciences,
University of Georgia,
Athens, Georgia 30602-3636 USA
Email Address:
gcelter@uga.edu
Web Address:
http://gce-lter.marsci.uga.edu/
Creators:
Organization: Georgia Coastal Ecosystems LTER Project
Address:
Dept. of Marine Sciences,
University of Georgia,
Athens, Georgia 30602-3636 USA
Email Address:
gcelter@uga.edu
Web Address:
http://gce-lter.marsci.uga.edu/
Individual: Dr. Christopher B. Craft
Organization: Indiana University at Bloomington
Address:
Indiana University - School of Public and Environmental Affairs,
Room 408. MSB II.,
702 N. Walnut Grove Ave.,
Bloomington, Indiana 47405 USA
Email Address:
ccraft@indiana.edu
Web Address:
http://www.indiana.edu/~craftlab/
Contacts:
Position: GCE-LTER Information Manager
Address:
Dept. of Marine Sciences,
University of Georgia,
Athens, Georgia 30602-3636 USA
Email Address:
gcelter@uga.edu
Associated Parties:
Individual: Dontrece Smith
Organization: University of Georgia Marine Institute
Email Address:
dtsmith@uga.edu
Role: field technician
Individual: Jennifer Desha
Organization: University of Georgia Marine Institute
Email Address:
jdesha@uga.edu
Role: field technician
Metadata Providers:
Organization: Georgia Coastal Ecosystems LTER Project
Address:
Dept. of Marine Sciences,
University of Georgia,
Athens, Georgia 30602-3636 USA
Email Address:
gcelter@uga.edu
Web Address:
http://gce-lter.marsci.uga.edu/

Temporal, Geographic and Taxonomic Coverage

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

Time Period
Begin:
2016-02-20
End:
2016-09-24
Geographic Region:
Description: Overall bounding box describing the geographic region within the Georgia Coastal Ecosystems LTER study domain represented in data set ALG-GCED-1610, based on the maximum geographic extents of all site polygons referenced in the data set
Bounding Coordinates:
Northern:   31.339834 Southern:   31.338952
Western:   -81.467197 Eastern:   -81.466189
Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'unitList' in ns 'http://www.xml-cml.org/schema/stmml-1.1' ('stmml:unitList')
        |     |     |  \___attribute 'schemaLocation' in ns 'http://www.w3.org/2001/XMLSchema-instance' ('xsi:schemaLocation') = 'http://www.xml-cml.org/schema/stmml-1.1 http://gce-lter.marsci.uga.edu/public/files/schemas/eml-210/stmml.xsd'
        |     |     |___text '\n        '
        |     |     |___comment 'note that the unitTypes here are taken from the eml-unitDictionary.xml'
        |     |     |___text '\n        '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.1' ('stmml:unit')
        |     |     |     |  \___attribute 'abbreviation' = 'ug/cm2'
        |     |     |     |  \___attribute 'id' = 'microgramsPerCentimeterSquared'
        |     |     |     |  \___attribute 'name' = 'microgramsPerCentimeterSquared'
        |     |     |     |  \___attribute 'unitType' = 'massDensity'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.1' ('stmml:description')
        |     |     |     |     |___text 'micrograms per square centimeter'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.1' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'nominalMonth'
        |     |     |     |  \___attribute 'name' = 'nominalMonth'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.1' ('stmml:description')
        |     |     |     |     |___text 'one month including a variable number of seconds'
        |     |     |     |___text '\n        '
        |     |     |___text '\n      '
        |     |___text '\n    '
        |___text '\n  '

Download as XML (in Ecological Metadata Language)
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