Above- and below-ground non-structural carbohydrates (NSC) in Spartina alterniflora from 6 permanant plots near the Georgia Coastal Ecosysterms LTER flux tower, on Sapelo Island in Georgia, USA

Summary Information
Data Package General Information:
Local Identifier: knb-lter-gce.625.7
Title: Above- and below-ground non-structural carbohydrates (NSC) in Spartina alterniflora from 6 permanant plots near the Georgia Coastal Ecosysterms LTER flux tower, on Sapelo Island in Georgia, USA
Alternate Identifier: ORG-GCET-1712.1.0
Alternate Identifier: doi:10.6073/pasta/c868deb66af9c0f72c9672f65b484995
Abstract:

We studied the dynamics of four non-structural carbohydrates (glucose, fructose, sucrose, and starch) and biomass in 8 different above- and below-ground tissues in Spartina alterniflora over the course of a year in a salt marsh on Sapelo Island, Georgia, USA. Tissue parts sampled included green leaves, green stems, yellow leaves, yellow stems, brown leaves and stem, flowers, belowground biomass from 0-10cm depth and belowground biomass from 10-30cm depth. Samples were collected from tall form S. alterniflora plots near the Georgia Coastal Ecosystems LTER flux tower site monthly between September 2013 and August 2014. This study was conducted to support the development of predictive, mechanistic models of Spartina by providing information on below-ground biomass and its dynamics, and in particular the storage of resources that can be used for spring re-growth.

Publication Date: 2018

Time Period
Begin:
2013-09-01
End:
2014-08-30

People and Organizations
Contact: GCE-LTER Information Manager [  email ]
Organization: Georgia Coastal Ecosystems LTER Project
Creator: Jung, Yeajin (University of Georgia)
Associate: Burd, Adrian B. (University of Georgia)

Data Entities
Data Table Name:
ORG-GCET-1712
Description:
Main data table for data set ORG-GCET-1712
Other Name:
ORG-GCET-1712_raw
Description:
Spreadsheet containing raw absorbance data
Other Name:
ORG-GCET-1712.kml
Description:
Google Earth Keyhole Markup Language file describing the geographic locations sampled in data set knb-lter-gce.625.7
Detailed Metadata

Data Entities


Data Table

Data: https://pasta.lternet.edu/package/data/eml/knb-lter-gce/625/7/7b4c690d3cb08cd037505cf455e5371a
Name: ORG-GCET-1712
Description: Main data table for data set ORG-GCET-1712
Number of Records: 96
Number of Columns: 39
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:

12/07/2017: new GCE Data Structure 1.1 created ("newstruct")

Substep 2  
Description:

12/07/2017: 96 rows imported from ASCII data file "ORG-GCET-1712.txt" ("imp_ascii")

Substep 3  
Description:

12/07/2017: 83 metadata fields in file header parsed ("parse_header")

Substep 4  
Description:

12/07/2017: data structure validated ("gce_valid")

Substep 5  
Description:

12/07/2017: converted text codes in flag column(s) Flag_Glucose_core1, Flag_SD_Glucose_core1, Flag_Glucose_core2, Flag_SD_Glucose_core2, Flag_Fructose_core1, Flag_SD_Fructose_core1, Flag_Fructose_core2, Flag_SD_Fructose_core2, Flag_Sucrose_core1, Flag_SD_Sucrose_core1, Flag_Sucrose_core2, Flag_SD_Sucrose_core2, Flag_Starch_core1, Flag_SD_Starch_core1, Flag_Starch_core2 and Flag_SD_Starch_core2 to QA/QC flags for data column(s) Glucose_core1, SD_Glucose_core1, Glucose_core2, SD_Glucose_core2, Fructose_core1, SD_Fructose_core1, Fructose_core2, SD_Fructose_core2, Sucrose_core1, SD_Sucrose_core1, Sucrose_core2, SD_Sucrose_core2, Starch_core1, SD_Starch_core1, Starch_core2 and SD_Starch_core2 and deleted flag source columns ("cols2flags")

Substep 6  
Description:

12/07/2017: updated 1 metadata fields in the Dataset sections ("addmeta")

Substep 7  
Description:

12/07/2017: imported Dataset, Project, Site, Study, Status, Supplement metadata descriptors from the GCE Metabase ("imp_gcemetadata")

Substep 8  
Description:

12/07/2017: updated 57 metadata fields in the Dataset, Project, Site, Status, Study, Supplement sections ("addmeta")

Substep 9  
Description:

12/07/2017: manually edited data set metadata ("ui_editmetadata")

Substep 10  
Description:

12/07/2017: Q/C Criteria of column DryWeight_core1 changed from "" to "x==NaN="T""; Q/C Criteria of column DryWeight_core2 changed from "" to "x==NaN="T" ("ui_editor")

Substep 11  
Description:

12/07/2017: Q/C flagging criteria applied for column(s) DryWeight_core1 and DryWeight_core2, "flags" field updated ("dataflag")

Substep 12  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 13  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 14  
Description:

12/07/2017: Q/C Criteria of column DryWeight_core1 changed from "x==NaN="T"" to "strcmp(x,NaN)="T" ("ui_editor")

Substep 15  
Description:

12/07/2017: Q/C flagging criteria applied for column(s) DryWeight_core1, "flags" field updated ("dataflag")

Substep 16  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 17  
Description:

12/07/2017: Q/C Criteria of column DryWeight_core1 changed from "strcmp(x,NaN)="T"" to "strcmp(x,"NaN")="T" ("ui_editor")

Substep 18  
Description:

12/07/2017: Q/C flagging criteria applied for column(s) DryWeight_core1, "flags" field updated ("dataflag")

Substep 19  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 20  
Description:

12/07/2017: Q/C Criteria of column DryWeight_core1 changed from "strcmp(x,"NaN")="T"" to "isnan(x)="T" ("ui_editor")

Substep 21  
Description:

12/07/2017: Q/C flagging criteria applied for column(s) DryWeight_core1, "flags" field updated ("dataflag")

Substep 22  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 23  
Description:

12/07/2017: Q/C Criteria of column DryWeight_core2 changed from "x==NaN="T"" to "isnan(x)="T" ("ui_editor")

Substep 24  
Description:

12/07/2017: Q/C flagging criteria applied for column(s) DryWeight_core2, "flags" field updated ("dataflag")

Substep 25  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 26  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 27  
Description:

12/07/2017: manually edited data set metadata ("ui_editmetadata")

Substep 28  
Description:

12/07/2017: updated 4 metadata fields ("addmeta")

Substep 29  
Description:

12/07/2017: updated 15 metadata fields in the Status, Data sections to reflect attribute metadata ("updatecols")

Substep 30  
Description:

12/07/2017: parsed and formatted metadata ("listmeta")

Substep 31  
Description:

12/07/2017: flags for columns DryWeight_core1, DryWeight_core2, Glucose_core1, SD_Glucose_core1, Glucose_core2, SD_Glucose_core2, Fructose_core1, SD_Fructose_core1, Fructose_core2, SD_Fructose_core2, Sucrose_core1, SD_Sucrose_core1, Sucrose_core2, SD_Sucrose_core2, Starch_core1, SD_Starch_core1, Starch_core2 and SD_Starch_core2 converted to data columns, flag codes updated in metadata ("flags2cols")

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). Automatically-assigned qualifier flags are reviewed graphically and revised or augmented as deemed appropriate by GCE information management staff, based on metadata information from the contributor, values of other measured variables, or statistical tests. 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: ORG-GCET-1712_1_0.CSV
Size: 18.06 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  
Tissue  
DryWeight_core1  
Flag_DryWeight_core1  
DryWeight_core2  
Flag_DryWeight_core2  
Glucose_core1  
Flag_Glucose_core1  
SD_Glucose_core1  
Flag_SD_Glucose_core1  
Glucose_core2  
Flag_Glucose_core2  
SD_Glucose_core2  
Flag_SD_Glucose_core2  
Fructose_core1  
Flag_Fructose_core1  
SD_Fructose_core1  
Flag_SD_Fructose_core1  
Fructose_core2  
Flag_Fructose_core2  
SD_Fructose_core2  
Flag_SD_Fructose_core2  
Sucrose_core1  
Flag_Sucrose_core1  
SD_Sucrose_core1  
Flag_SD_Sucrose_core1  
Sucrose_core2  
Flag_Sucrose_core2  
SD_Sucrose_core2  
Flag_SD_Sucrose_core2  
Starch_core1  
Flag_Starch_core1  
SD_Starch_core1  
Flag_SD_Starch_core1  
Starch_core2  
Flag_Starch_core2  
SD_Starch_core2  
Flag_SD_Starch_core2  
Definition: Year sample was collected Month sample was collected Type of tissue analyzed Dry weight of tissue in core 1 QA/QC flags for Dry weight of tissue in core 1 (flagging criteria, where "x" is DryWeight_core1: isnan(x)="T") Dry weight of tissue in core 2 QA/QC flags for Dry weight of tissue in core 2 (flagging criteria, where "x" is DryWeight_core2: isnan(x)="T") Average dry weight of glucose in core 1 (n=3) QA/QC flags for Average dry weight of glucose in core 1 (n=3) (flagging criteria, where "x" is Glucose_core1: manual) Standard Deviation of glucose in core 1 QA/QC flags for Standard Deviation of glucose in core 1 (flagging criteria, where "x" is SD_Glucose_core1: manual) Average dry weight of glucose in core 2 (n=3) QA/QC flags for Average dry weight of glucose in core 2 (n=3) (flagging criteria, where "x" is Glucose_core2: manual) Standard Deviation of glucose in core 2 QA/QC flags for Standard Deviation of glucose in core 2 (flagging criteria, where "x" is SD_Glucose_core2: manual) Average dry weight of fructose in core 1 (n=3) QA/QC flags for Average dry weight of fructose in core 1 (n=3) (flagging criteria, where "x" is Fructose_core1: manual) Standard Deviation of fructose in core 1 QA/QC flags for Standard Deviation of fructose in core 1 (flagging criteria, where "x" is SD_Fructose_core1: manual) Average dry weight of fructose in core 2 (n=3) QA/QC flags for Average dry weight of fructose in core 2 (n=3) (flagging criteria, where "x" is Fructose_core2: manual) Standard Deviation of fructose in core 2 QA/QC flags for Standard Deviation of fructose in core 2 (flagging criteria, where "x" is SD_Fructose_core2: manual) Average dry weight of sucrose in core 1 (n=3) QA/QC flags for Average dry weight of sucrose in core 1 (n=3) (flagging criteria, where "x" is Sucrose_core1: manual) Standard Deviation of sucrose in core 1 QA/QC flags for Standard Deviation of sucrose in core 1 (flagging criteria, where "x" is SD_Sucrose_core1: manual) Average dry weight of sucrose in core 2 (n=3) QA/QC flags for Average dry weight of sucrose in core 2 (n=3) (flagging criteria, where "x" is Sucrose_core2: manual) Standard Deviation of sucrose in core 2 QA/QC flags for Standard Deviation of sucrose in core 2 (flagging criteria, where "x" is SD_Sucrose_core2: manual) Average dry weight of starch in core 1 (n=3) QA/QC flags for Average dry weight of starch in core 1 (n=3) (flagging criteria, where "x" is Starch_core1: manual) Standard Deviation of starch in core 1 QA/QC flags for Standard Deviation of starch in core 1 (flagging criteria, where "x" is SD_Starch_core1: manual) Average dry weight of starch in core 2 (n=3) QA/QC flags for Average dry weight of starch in core 2 (n=3) (flagging criteria, where "x" is Starch_core2: manual) Standard Deviation of starch in core 2 QA/QC flags for Standard Deviation of starch in core 2 (flagging criteria, where "x" is SD_Starch_core2: manual)
Storage Type: integer  
string  
string  
float  
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float  
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float  
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float  
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float  
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float  
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float  
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float  
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float  
string  
float  
string  
float  
string  
float  
string  
float  
string  
float  
string  
float  
string  
float  
string  
float  
string  
float  
string  
Measurement Type: interval nominal nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal ratio nominal
Measurement Values Domain:
Unit nominalYear
Precision 1
Type whole
Definition Month sample was collected
Definition Type of tissue analyzed
Unit gram
Precision 0.01
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code T
Definition Tissue not collected
Source
Unit gram
Precision 0.01
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code T
Definition Tissue not collected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
Unit gram
Precision 0.0001
Type real
Allowed Values and Definitions
Enumerated Domain  
Code Definition
Code N
Definition Not Detected
Source
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)
 
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)
 
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: ORG-GCET-1712_raw
Entity Type: Zip_Archive
Description: Spreadsheet containing raw absorbance data
Physical Structure Description:
Object Name: ORG-GCET-1712_raw.zip
Size: 283 kb
Externally Defined Format:
Format Name: application/zip
Data: https://pasta.lternet.edu/package/data/eml/knb-lter-gce/625/7/9fb6881c0624cc8e9f46bfc3b47138ab

Non-Categorized Data Resource

Name: ORG-GCET-1712.kml
Entity Type: KML
Description: Google Earth Keyhole Markup Language file describing the geographic locations sampled in data set knb-lter-gce.625.7
Physical Structure Description:
Object Name: ORG-GCET-1712.kml
Externally Defined Format:
Format Name: application/vnd.google-earth.kml+xml
Data: https://pasta.lternet.edu/package/data/eml/knb-lter-gce/625/7/aa105db0de6ed2ae3ff1b5b4336be602

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, Spartina, fructose, GCE, Georgia Coastal Ecosystems, glucose, LTER, Non-structural carbohydrates, starch, sucrose
GCE-LTER Species List Angiospermae, Lilianae, Magnoliopsida, Plantae, Poaceae, Poales, Spartina alterniflora, Spermatophytina, Streptophyta, Tracheophyta, Viridaeplantae
LTER Controlled Vocabulary aboveground biomass, belowground biomass, carbohydrates, organic matter, primary production
LTER Core Research Areas Organic Matter

Methods and Protocols

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

Protocols and/or Procedures
Description:

Sample Collection

Two cores were collected from locations randomly selected from within 6 long-term sampling sites. Above-ground samples were clipped at the ground level and the below-ground samples were collected using a 7.5 cm diameter PVC pipe. Cores were taken to a depth of 30 cm, taking care to preserve above-ground shoots; cores were collected such that there were 1 or 2 above-ground shoots per core. Samples were kept at 4 °C for one night. On the next day, the cores were gently washed with flowing fresh water over an 800 µm sieve to remove mud, then dried in an oven at 60 °C for 3 days.

Description:

Sample Preparation

Above-ground tissues were separated into 6 distinct categories; green leaves, green stems, senescing yellow leaves, senescing yellow stems, flowers, and brown leaves and stems representing dead material. Only live roots and rhizomes were used and these were distinguished using the method described by Valiela et al. (1976). Below-ground cores were divided into 2 categories; shallow (0–10 cm) and deep (10–30 cm) parts. Each component of the plant biomass was weighed, and approximately 4 g of each tissue part was ground to a fine powder using a ball mill (model 8000-D Mixer/Mill, Spex Sample Prep, Metuchen, NJ) until the material passed through a 1 mm screen. Ground samples were stored in airtight scintillation vials.

Instrument(s): ball mill - model 8000-D Mixer/Mill, Spex Sample Prep, Metuchen, NJ
Description:

Sample Analysis

Non-structural carbohydrate (NSC) content in samples was analyzed using a method modified from Zhao et al. (2010). Approximately 16 mg of each dried powder sample were placed in a 1.5 mL micro-centrifuge tube. Sugars in samples were solubilized using 80% ethanol in an 80 °C water bath and the extraction process repeated three times to ensure all solubilized sugars from the samples were collected. The final extract volume was centrifuged for 15 min at 13,500 × g. Three replicates of supernatant were incubated with a sequence of enzymes in 96-well plates to quantify glucose, fructose, and sucrose content in each sample. Between extraction of each soluble NSC process, the tube containing supernatant was placed in boiling water to halt any digestion of sugars. Starch, the water-insoluble sugar remaining in the pellet after removal of the supernatant, was solubilized following the procedure specified in Zhao et al. (2010) and then reduced to glucose. The absorbance of each sample was determined photometrically at 340 nm using a 96-Well plate reader (Flexstation3 Benchtop Multi-mode Multiplate Reader, Molecular Devices, Sunnyvale, CA). NSC concentrations were quantified according to standard curves using d-(+)-glucose standards that were run with each plate.

Instrument(s): Flexstation3 Benchtop Multi-mode Multiplate Reader, Molecular Devices, Sunnyvale, CA
Sampling Area and Study Extent
Sampling Description:

NSC

6 long-term tall type Spartina sampling sites near flux tower 

Two cores were collected from locations randomly selected from within 6 long-term sampling sites. Above-ground tissues were separated into 6 distinct categories; green leaves, green stems, senescing yellow leaves, senescing yellow stems, flowers, and brown leaves and stems representing dead material. Below-ground cores were divided into 2 categories; shallow (0–10 cm) and deep (10–30 cm) parts. Non-structural carbohydrate content in samples was analyzed using a method modified from Zhao et al. (2010).

Two cores were collected from locations randomly selected from within 6 long-term sampling sites. Above-ground samples were clipped at the ground level and the below-ground samples were collected using a 7.5 cm diameter PVC pipe. Cores were taken to a depth of 30 cm, taking care to preserve above-ground shoots; cores were collected such that there were 1 or 2 above-ground shoots per core. Samples were kept at 4 °C for one night. On the next day, the cores were gently washed with flowing fresh water over an 800 µm sieve to remove mud, then dried in an oven at 60 °C for 3 days.

Sampling Extent:

Time Period
Begin:
2013-09-01
End:
2014-08-30
Sampling Extent:
Geographic Region:
Description: GCE Study Site GCE_Flux -- GCE Flux Tower Marsh, Sapelo Island, Georgia. Spartina alterniflora marsh on western Sapelo Island where the GCE-LTER Eddy Covariance Flux Tower is sited, bounded by the Duplin River and Barn Creek
Bounding Coordinates:
Northern:   31.456590 Southern:   31.436700
Western:   -81.288627 Eastern:   -81.272563

These methods, instrumentation, and/or protocols apply to the data table ORG-GCET-1712:

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:

12/07/2017: new GCE Data Structure 1.1 created ("newstruct")

Substep 2  
Description:

12/07/2017: 96 rows imported from ASCII data file "ORG-GCET-1712.txt" ("imp_ascii")

Substep 3  
Description:

12/07/2017: 83 metadata fields in file header parsed ("parse_header")

Substep 4  
Description:

12/07/2017: data structure validated ("gce_valid")

Substep 5  
Description:

12/07/2017: converted text codes in flag column(s) Flag_Glucose_core1, Flag_SD_Glucose_core1, Flag_Glucose_core2, Flag_SD_Glucose_core2, Flag_Fructose_core1, Flag_SD_Fructose_core1, Flag_Fructose_core2, Flag_SD_Fructose_core2, Flag_Sucrose_core1, Flag_SD_Sucrose_core1, Flag_Sucrose_core2, Flag_SD_Sucrose_core2, Flag_Starch_core1, Flag_SD_Starch_core1, Flag_Starch_core2 and Flag_SD_Starch_core2 to QA/QC flags for data column(s) Glucose_core1, SD_Glucose_core1, Glucose_core2, SD_Glucose_core2, Fructose_core1, SD_Fructose_core1, Fructose_core2, SD_Fructose_core2, Sucrose_core1, SD_Sucrose_core1, Sucrose_core2, SD_Sucrose_core2, Starch_core1, SD_Starch_core1, Starch_core2 and SD_Starch_core2 and deleted flag source columns ("cols2flags")

Substep 6  
Description:

12/07/2017: updated 1 metadata fields in the Dataset sections ("addmeta")

Substep 7  
Description:

12/07/2017: imported Dataset, Project, Site, Study, Status, Supplement metadata descriptors from the GCE Metabase ("imp_gcemetadata")

Substep 8  
Description:

12/07/2017: updated 57 metadata fields in the Dataset, Project, Site, Status, Study, Supplement sections ("addmeta")

Substep 9  
Description:

12/07/2017: manually edited data set metadata ("ui_editmetadata")

Substep 10  
Description:

12/07/2017: Q/C Criteria of column DryWeight_core1 changed from "" to "x==NaN="T""; Q/C Criteria of column DryWeight_core2 changed from "" to "x==NaN="T" ("ui_editor")

Substep 11  
Description:

12/07/2017: Q/C flagging criteria applied for column(s) DryWeight_core1 and DryWeight_core2, "flags" field updated ("dataflag")

Substep 12  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 13  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 14  
Description:

12/07/2017: Q/C Criteria of column DryWeight_core1 changed from "x==NaN="T"" to "strcmp(x,NaN)="T" ("ui_editor")

Substep 15  
Description:

12/07/2017: Q/C flagging criteria applied for column(s) DryWeight_core1, "flags" field updated ("dataflag")

Substep 16  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 17  
Description:

12/07/2017: Q/C Criteria of column DryWeight_core1 changed from "strcmp(x,NaN)="T"" to "strcmp(x,"NaN")="T" ("ui_editor")

Substep 18  
Description:

12/07/2017: Q/C flagging criteria applied for column(s) DryWeight_core1, "flags" field updated ("dataflag")

Substep 19  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 20  
Description:

12/07/2017: Q/C Criteria of column DryWeight_core1 changed from "strcmp(x,"NaN")="T"" to "isnan(x)="T" ("ui_editor")

Substep 21  
Description:

12/07/2017: Q/C flagging criteria applied for column(s) DryWeight_core1, "flags" field updated ("dataflag")

Substep 22  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 23  
Description:

12/07/2017: Q/C Criteria of column DryWeight_core2 changed from "x==NaN="T"" to "isnan(x)="T" ("ui_editor")

Substep 24  
Description:

12/07/2017: Q/C flagging criteria applied for column(s) DryWeight_core2, "flags" field updated ("dataflag")

Substep 25  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 26  
Description:

12/07/2017: Q/C flagging criteria applied, "flags" field updated ("dataflag")

Substep 27  
Description:

12/07/2017: manually edited data set metadata ("ui_editmetadata")

Substep 28  
Description:

12/07/2017: updated 4 metadata fields ("addmeta")

Substep 29  
Description:

12/07/2017: updated 15 metadata fields in the Status, Data sections to reflect attribute metadata ("updatecols")

Substep 30  
Description:

12/07/2017: parsed and formatted metadata ("listmeta")

Substep 31  
Description:

12/07/2017: flags for columns DryWeight_core1, DryWeight_core2, Glucose_core1, SD_Glucose_core1, Glucose_core2, SD_Glucose_core2, Fructose_core1, SD_Fructose_core1, Fructose_core2, SD_Fructose_core2, Sucrose_core1, SD_Sucrose_core1, Sucrose_core2, SD_Sucrose_core2, Starch_core1, SD_Starch_core1, Starch_core2 and SD_Starch_core2 converted to data columns, flag codes updated in metadata ("flags2cols")

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). Automatically-assigned qualifier flags are reviewed graphically and revised or augmented as deemed appropriate by GCE information management staff, based on metadata information from the contributor, values of other measured variables, or statistical tests. 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: Yeajin Jung
Organization: University of Georgia
Address:
Dept. of Marine Sciences,
University of Georgia,
Athens, Georgia 30602-3636 USA
Email Address:
yeajin84@uga.edu
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: Dr. Adrian B. Burd
Organization: University of Georgia
Email Address:
adrianb@uga.edu
Id: http://orcid.org/0000-0001-6345-8770
Role: thesis advisor
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:
2013-09-01
End:
2014-08-30
Geographic Region:
Description: Overall bounding box describing the geographic region within the Georgia Coastal Ecosystems LTER study domain represented in data set ORG-GCET-1712, based on the maximum geographic extents of all site polygons referenced in the data set
Bounding Coordinates:
Northern:   31.456590 Southern:   31.436700
Western:   -81.288627 Eastern:   -81.272563
Taxonomic Range:
Classification:
Rank Name: Kingdom
Rank Value: Plantae
Classification:
Rank Name: Subkingdom
Rank Value: Viridaeplantae
Classification:
Rank Name: Infrakingdom
Rank Value: Streptophyta
Classification:
Rank Name: Division
Rank Value: Tracheophyta
Classification:
Rank Name: Subdivision
Rank Value: Spermatophytina
Classification:
Rank Name: Infradivision
Rank Value: Angiospermae
Classification:
Rank Name: Class
Rank Value: Magnoliopsida
Classification:
Rank Name: Superorder
Rank Value: Lilianae
Classification:
Rank Name: Order
Rank Value: Poales
Classification:
Rank Name: Family
Rank Value: Poaceae
Classification:
Rank Name: Genus
Rank Value: Spartina
Classification:
Rank Name: Species
Rank Value: Spartina alterniflora
Common Name: smooth cordgrass, Atlantic cordgrass, saltmarsh cordgrass
Other Metadata

Download as XML (in Ecological Metadata Language)
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