Data Package Metadata View Summary

Benthic algae chlorophyll measurements for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.

General Information

Data Package:

Local Identifier:

knb-lter-pie.197.5

Title:

Benthic algae chlorophyll measurements for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.

Alternate Identifier:

DOI PLACE HOLDER

Abstract:

Benthic Algae (Chlorophyll a) Sampling Protocol for TIDE
FIELD
Frequency: Monthly, May thru September
Field Equipment (stored in the TIDE benthic algae tool box):
50 ml syringes with tips cut off, knives, rulers, labeled 50 ml centrifuge tubes, extra labels and centrifuge tubes, pencil
At each plant transect collect the following number of samples in each habitat: 3 mudflat (MF), 3 filamentous algae (FA), 3 tall creekbank Spartina alterniflora (TSA), 3 Spartina patens (SP), 3 short Spartina alterniflora (SSA).
Habitat:
Collect samples at low tide in order to access mudflat, filamentous algae, tall creekbank S. alterniflora and S. patens. , FA, and TSA habitat types.
Use transect as guideline for picking sample locations, but do not work directly along the transect line.
Choose general sampling location and toss syringe to “haphazardly” pick exact spot.
To collect sample: slowly push down syringe while pulling up on the plunger (try not to compress the sample). Try to get as far down as possible and then slowly pull the tube out of the substrate. Pull the plunger out and stick it into the opposite end of the syringe. Using ruler to measure, push out 2 cm of sample into the appropriately labeled centrifuge tube. (Be careful to measure two centimeters as carefully as possible each time. Calculations of chlorophyll after analysis assume equal volumes of sediment in each sample.)
MF: Take sample in exposed horizontal mud flats along creek channel during low tide. Avoid inserting syringe into an area with root masses and fibers, it is generally very easy to sample in the mud flats.
FA: Take sample along creek wall below TSA roots layer in the obvious filamentous algal zone.
TSA: Same as mudflats.
SP &amp; SSA: Sampling is more difficult, because of the dense roots. Cut around cylinder with knife as you are inserting syringe into ground. Once syringe is inserted far enough cut a cone shape underneath syringe with knife and pull out syringe at an angle in order not to lose the sample.
Collection takes about a half day per creek with two people.
Once samples are collected, wipe off as much mud on the outside of the tubes and store in labeled plastics bags. Samples must remain frozen until analysis.
LAB EXTRACTION
Step 1: Extraction (typically done in the pm the day before analysis on spectrophotometer)
Supplies:
50-ml polypropylene centrifuge tubes containing sample (frozen and in the dark)
100% acetone
90% acetone
Coolers with ice
Re-pippeter
Latex (non-nitrile) gloves
Considerations:
Chlorophyll degrades easily. As much as possible, keep samples cool and dark.
Work in a hood to minimize your exposure to acetone fumes and cap samples tightly
when not in use. Acetone eats many plastics so be mindful of the materials you are using
to store and transfer samples. Acetone will also wash away sharpie- so keep track of
sample numbers and protect your labels. Avoid using acid-washed equipment to
minimize potential acid-contamination of samples. Length of extraction should be
around 16 hours, so plan to time your sample prep and analysis accordingly. Prep only
the amount of samples you can feasibly analyze in one sitting. Usually no more than 40-
50 samples at a time.
Prep samples with acetone:
1. Allow samples to thaw at room temperature for about two hours before putting in
coolers. Samples should be thawed, but cool to the touch.
2. Clean any excess mud off of sample containers and transfer thawed samples to
coolers with ice
3. Store acetone solution in coolers on ice
4. Under hood, use a re-pippeter to add 25mls of 100% acetone to each tube
5. Shake each sample vigerously by hand to break up sediment at the bottom of each
tube
6. Place tubes back on ice in cooler. Samples maybe sonicated or shock chilled to further break algal cells.
7. Centrifuge sample prior to reading on the spectophotometer.
Reference creeks in all years are West and Nelson
Nutrient Enriched creeks are Sweeney and Clubhead.
Sweeney was fertilized every summer from 2004-2016. Clubhead was fertilized in 2005 and then from 2009-2016.
All major creeks have two branches determined by direction at confluence while facing upstream (Left or Right).
Plant transects run perpendicular to creeks at various points with a front pole at the creek bank and a back pole an the high marsh. Transects are in the order of 1, 2, 4, 3 or blue, green, red, yellow from confluence of branch.
MF= Mud Flat
TSA= Tall Spartina alterniflora
SP= Spartina patens
SSA=Short Spartina alterniflora
FA= Filamentous algae

Purpose:

Short Name:

LTE-TIDE-BenChl

Publication Date:

2022-01-31

Language:

English

For more information:
Visit:	https://pie-lter.ecosystems.mbl.edu/content/benthic-algae-chlorophyll-measurements-rowley-river-tidal-creeks-associated-long-term-fertil
Visit:	DOI PLACE HOLDER

Time Period

Begin:

2003-06-01

End:

2021-08-01

People and Organizations
Contact:	Plum Island Ecosystems LTER
Creator:	Deegan, Linda
Associate:	Morkeski, Kate
Associate:	Sullivan, Hillary

Data Entities
Data Table Name:	LTE-TIDE-BenChl_csv
Description:	Benthic algae chlorophyll measurements for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.
Other Name:	LTE-TIDE-BenChl_xls
Description:	Excel metadata and data file associated with the csv data source file. Excel file after downloading is to be used for adding/editing new metadata and data.

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/knb-lter-pie/197/5/b0fb7dc2b9f70e57ca93efa51d7eece2
Name:	LTE-TIDE-BenChl_csv
Description:	Benthic algae chlorophyll measurements for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.
Number of Records:	8023
Number of Columns:	11

Table Structure

Object Name:

LTE-TIDE-BenChl_ver5.csv

Size:

312628

Authentication:

b0cad2742f530a9460aa98e5b5412dda Calculated By MD5

Authentication:

7e24af76ab1a526b11746d989313e4359822f205 Calculated By SHA-1

Text Format:

Number of Header Lines:

Number of Foot Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:

Table Column Descriptions

Year

Treatment

Creek

Month

Branch

Transect

Replicate

Habitat

Chla areal

Phaeo areal

Comment

Column Name:

Year

Treatment

Creek

Month

Branch

Transect

Replicate

Habitat

Chla areal

Phaeo areal

Comment

Definition:

Year Sampled

Indicates whether the creek was sampled Prior to nutrient enrichment (P), during nutrient enrichment enriched (N), always a Reference/Control (R) or Post nutrient enrichment or Recovery (RN).

Creek Sampled

Month of Sampling

Branch Sampled

Transect Sampled or Area Sampled

Replicate of Sample

Habitat Sampled

Areal concentration of benthic chlorophyll a

Areal concentraion of phaeophytin

Notes on the sample or analysis

Storage Type:

date

string

Measurement Type:

dateTime

nominal

ratio

nominal

Measurement Values Domain:

Format	YYYY
Precision

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	N
Definition	Nutrient enriched in this year
Source

Code Definition

Code	C
Definition	Never Nutrient Enriched
Source

Code Definition

Code	R
Definition	Recovering from Nutrient enrichment.
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	SW
Definition	Sweeney- Nutrient Enriched
Source

Code Definition

Code	NE
Definition	Nelson- Nutrient Enriched
Source

Code Definition

Code	WE
Definition	West- Reference
Source

Code Definition

Code	CL
Definition	Clubhead- Reference
Source

Definition

Month of Sampling

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	L
Definition	Left Branch
Source

Code Definition

Code	R
Definition	Right Branch
Source

Code Definition

Code	C
Definition	Confluence
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1
Definition	Transect 1
Source

Code Definition

Code	2
Definition	Transect
Source

Code Definition

Code	3
Definition	Transect 3
Source

Code Definition

Code	4
Definition	Transect 4
Source

Code Definition

Code	0
Definition	Confluence
Source

Code Definition

Code	25
Definition	25 m mark
Source

Code Definition

Code	50
Definition	50 m mark
Source

Code Definition

Code	75
Definition	75 m mark
Source

Code Definition

Code	100
Definition	100 m mark
Source

Code Definition

Code	125
Definition	125 m mark
Source

Code Definition

Code	150
Definition	150 m mark
Source

Code Definition

Code	175
Definition	175 m mark
Source

Code Definition

Code	250
Definition	250 m mark
Source

Code Definition

Code	350
Definition	350 m mark
Source

Code Definition

Code	450
Definition	450 m mark
Source

Definition

Replicate of Sample

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	MF
Definition	Mud Flat
Source

Code Definition

Code	TSA
Definition	Tall Spartina alterniflora
Source

Code Definition

Code	SP
Definition	Spartina patens
Source

Code Definition

Code	SSA
Definition	Short Spartina alterniflora
Source

Code Definition

Code	FA
Definition	Filamentous algae
Source

Unit	milligramPerMeterSquared
Type	real

Unit	milligramPerMeterSquared
Type	real

Definition

Notes on the sample or analysis

Missing Value Code:

Code	NA
Expl	missing

Code	NA
Expl	missing

Code	NA
Expl	missing

Code	NA
Expl	missing

Code	NA
Expl	missing

Code	NA
Expl	missing

Code	NA
Expl	missing

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Non-Categorized Data Resource

Name:

LTE-TIDE-BenChl_xls

Entity Type:

document

Description:

Excel metadata and data file associated with the csv data source file. Excel file after downloading is to be used for adding/editing new metadata and data.

Physical Structure Description:

Object Name:

LTE-TIDE-BenChl_ver5.xlsx

Size:

444909

Authentication:

77d8699c72e28dd11430feefdc9fb49b Calculated By MD5

Authentication:

0eb0f0cbd6ed6081473aa92520c8cb6eb11e06b8 Calculated By SHA-1

Externally Defined Format:

Format Name:

application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

Data:

https://pasta-s.lternet.edu/package/data/eml/knb-lter-pie/197/5/4c533e04b2974b083ddb09b587edf1c6

Data Package Usage Rights

Data Policies

PIE LTER Data Use Agreement

This work is licensed under the Creative Commons Attribution 4.0 International License, CC BY - Attribution. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

The re-use of scientific data has the potential to greatly increase communication, collaboration and synthesis within and among disciplines, and thus is fostered, supported and encouraged. Permission to use this dataset is granted to the Data User free of charge subject to the following terms:

1) Citation. It is considered a matter of professional ethics to acknowledge the work of other scientists. Thus, the Data User will properly cite the Data Set in any publications or in the metadata of any derived data products that were produced using the Data Set. Citation should take the following general form: Creator, Year of Data Publication, Title of Dataset, Publisher, Dataset identifier.
For example: Giblin, Anne; Hopkinson, Charles (2000): Rates of benthic metabolism and nutrient cycling in the Parker and Rowley Rivers of the Plum Island Sound estuary. Plum Island Ecosystems LTER, Long Term Ecological Research Network. http://dx.doi.org/10.6073/pasta/17fa8b4fef50c7b85cac3d61482a7cb6
2) Acknowledgement. The Data User should acknowledge any institutional support or specific funding awards referenced in the metadata accompanying this dataset in any publications where the Data Set contributed significantly to its content. Acknowledgements should identify the supporting party, the party that received the support, and any identifying information such as grant numbers. The Data User should contact the Data Set Contact to ensure the appropriate Granting Programs are acknowledged.
For example: Data sets were provided by the Plum Island Ecosystems LTER. This material is based upon funding supported by the National Science Foundation under Grants #OCE-9726921, OCE-0423565, OCE-1058747, OCE-1238212, OCE-1637630.
3) Notification. The Data User will notify the Data Set Contact when any derivative work or publication based on or derived from the Data Set is distributed. The Data User will provide the data contact with two reprints of any publications resulting from use of the Data Set and will provide copies, or on-line access to, any derived digital products. Notification will include an explanation of how the Data Set was used to produce the derived work.
4) Collaboration. The Data Set has been released in the spirit of open scientific collaboration. Data Users are thus strongly encouraged to consider consultation, collaboration and/or co-authorship with the Data Set Creator.
5) Disclaimer. While substantial efforts are made to ensure the accuracy of data and documentation contained in this Data Set, complete accuracy of data and metadata cannot be guaranteed. All data and metadata are made available "as is". The Data User holds all parties involved in the production or distribution of the Data Set harmless for damages resulting from its use or interpretation.

Keywords

By Thesaurus:
Core Areas	Primary Production, Inorganic Nutrients
LTER Controlled Vocabulary	creek, marshes, Spartina, chlorophyll, nutrients, tidal creek, benthic, mud Flat, algae, PIE LTER, Plum Island Ecosystems, primary production

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:

Benthic Algae (Chlorophyll A) Sampling Protocol for TIDE
FIELD
Frequency: Monthly, May thru September
Field Equipment (stored in the TIDE benthic algae tool box):
50 ml syringes with tips cut off, knives, rulers, labeled 50 ml centrifuge tubes, extra labels and centrifuge tubes, pencil
At each plant transect collect the following number of samples in each habitat: 3 mudflat (MF), 3 filamentous algae (FA), 3 tall creekbank Spartina alterniflora (TSA), 3 Spartina patens (SP), 3 short Spartina alterniflora (SSA).
Habitat:
Collect samples at low tide in order to access mudflat, filamentous algae, tall creekbank S. alterniflora and S. patens. , FA, and TSA habitat types.
Use transect as guideline for picking sample locations, but do not work directly along the transect line.
Choose general sampling location and toss syringe to “haphazardly” pick exact spot.
To collect sample: slowly push down syringe while pulling up on the plunger (try not to compress the sample). Try to get as far down as possible and then slowly pull the tube out of the substrate. Pull the plunger out and stick it into the opposite end of the syringe. Using ruler to measure, push out 2 cm of sample into the appropriately labeled centrifuge tube. (Be careful to measure two centimeters as carefully as possible each time. Calculations of chlorophyll after analysis assume equal volumes of sediment in each sample.)
MF: Take sample in exposed horizontal mud flats along creek channel during low tide. Avoid inserting syringe into an area with root masses and fibers, it is generally very easy to sample in the mud flats.
FA: Take sample along creek wall below TSA roots layer in the obvious filamentous algal zone.
TSA: Same as mudflats.
SP &amp; SSA: Sampling is more difficult, because of the dense roots. Cut around cylinder with knife as you are inserting syringe into ground. Once syringe is inserted far enough cut a cone shape underneath syringe with knife and pull out syringe at an angle in order not to lose the sample.
Collection takes about a half day per creek with two people.
Once samples are collected, wipe off as much mud on the outside of the tubes and store in labeled plastics bags. Samples must remain frozen until analysis.
LAB EXTRACTION
Step 1: Extraction (typically done in the pm the day before analysis on spectrophotometer)
Supplies:
50-ml polypropylene centrifuge tubes containing sample (frozen and in the dark)
100% acetone
90% acetone
Coolers with ice
Re-pippeter
Latex (non-nitrile) gloves
Considerations:
Chlorophyll degrades easily. As much as possible, keep samples cool and dark.
Work in a hood to minimize your exposure to acetone fumes and cap samples tightly when not in use. Acetone eats many plastics so be mindful of the materials you are using
to store and transfer samples. Acetone will also wash away sharpie- so keep track of sample numbers and protect your labels. Avoid using acid-washed equipment to
minimize potential acid-contamination of samples. Length of extraction should be around 16 hours, so plan to time your sample prep and analysis accordingly. Prep only
the amount of samples you can feasibly analyze in one sitting. Usually no more than 40- 50 samples at a time.
Prep samples with acetone:
1. Allow samples to thaw at room temperature for about two hours before putting in coolers. Samples should be thawed, but cool to the touch.
2. Clean any excess mud off of sample containers and transfer thawed samples to coolers with ice
3. Store acetone solution in coolers on ice
4. Under hood, use a re-pippeter to add 25mls of 100% acetone to each tube
5. Shake each sample vigerously by hand to break up sediment at the bottom of each tube
6. Place tubes back on ice in cooler. Samples maybe sonicated or shock chilled to further break algal cells.
7. Centrifuge sample prior to reading on the spectophotometer.
Reference creeks in all years are West and Nelson
Nutrient Enriched creeks are Sweeney and Clubhead.
Sweeney was fertilized every summer from 2004-2016. Clubhead was fertilized in 2005 and then from 2009-2016.
All major creeks have two branches determined by direction at confluence while facing upstream (Left or Right).
Plant transects run perpendicular to creeks at various points with a front pole at the creek bank and a back pole an the high marsh. Transects are in the order of 1, 2, 4, 3 or blue, green, red, yellow from confluence of branch.
MF= Mud Flat
TSA= Tall Spartina alterniflora
SP= Spartina patens
SSA=Short Spartina alterniflora
FA= Filamentous algae

People and Organizations

Publishers:

Organization:

Environmental Data Initiative

Email Address:

info@environmentaldatainitiative.org

Web Address:

https://environmentaldatainitiative.org

Id:

https://ror.org/0330j0z60

Creators:

Individual:

Linda Deegan

Address:

Woodwell Climate Research Center,

Falmouth, MA 02540 US

Phone:

508-444-1557 (voice)

Email Address:

ldeegan@woodwellclimate.org

Id:

http://orcid.org/0000-0002-1017-9599

Contacts:

Organization:

Plum Island Ecosystems LTER

Web Address:

http://pie-lter.ecosystems.mbl.edu/

Associated Parties:

Individual:

Kate Morkeski

Address:

Marine Biological Laboratory, 7 MBL Street,

Woods Hole, MA 02543 US

Phone:

(508) 289-7772 (voice)

Phone:

(508) 457-1548 (facsimile)

Email Address:

kmorkeski@mbl.edu

Role:

associated researcher

Individual:

Hillary Sullivan

Address:

Woodwell Climate Research Center,

Falmouth, MA 02540 US

Phone:

(508)-444-1527 (voice)

Email Address:

hsullivan@woodwellclimate.org

Role:

associated researcher

Metadata Providers:

Organization:

Plum Island Ecosystems LTER

Web Address:

http://pie-lter.ecosystems.mbl.edu/

Temporal, Geographic and Taxonomic Coverage

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

Time Period

Begin:

2003-06-01

End:

2021-08-01

Sampling Site:

Description:

"Sweeney Creek", off Rowley River, Ipswich, MA

Site Coordinates:

Longitude (degree):

-70.847198486328

Latitude (degree):

42.722244262695

Sampling Site:

Description:

West Creek, off Rowley River, Rowley, MA.

Site Coordinates:

Longitude (degree):

-70.849662780762

Latitude (degree):

42.737945556641

Sampling Site:

Description:

Clubhead Creek off Rowley River, Rowley, MA.

Site Coordinates:

Longitude (degree):

-70.838386535645

Latitude (degree):

42.739978790283

Sampling Site:

Description:

Nelson Island Creek, off Rowley River, Rowley,

Site Coordinates:

Longitude (degree):

-70.833152770996

Latitude (degree):

42.742115020752

Project

Maintenance

Maintenance:

Description:

Version 01: January 27, 2012, updated data and metadata. Used MarcrosExportEML_HTML (working)pie_excel2007.xlsm 1/18/12 4:51 PM for QA/QC to EML 2.1.0.
Version 02: June 20, 2013, data and metadata updated to comply with importation to Drupal and LTER PASTA. Research location name and description updated.Used MarcrosExportEML_HTML (working)pie_excel2007.xlsm 3/14/13 12:02 PM for QA/QC to EML 2.1.0
Version 03: August 1, 2019, data and metadata updates to comply with importation to DEIMS7 and LTER Data Portal. Used MarcrosExportEML_HTML (working)pie_excel2007_Jun2019.xlsm 6/7/19 12:58 PM for QA/QC to EML 2.1.0
Version 04: August 2. 2019 updated publication date to reflect date of new data submission
Version 05: January 27, 2022 updated publication date to reflect date of new data submission

Frequency:

Other Metadata

Additional Metadata

additionalMetadata
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        |     |     |___text '\n        '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.1' ('stmml:unit')
        |     |     |     |  \___attribute 'abbreviation' = 'mg/m²'
        |     |     |     |  \___attribute 'constantToSI' = '0'
        |     |     |     |  \___attribute 'id' = 'milligramPerMeterSquared'
        |     |     |     |  \___attribute 'multiplierToSI' = '0.000001'
        |     |     |     |  \___attribute 'name' = 'milligramPerMeterSquared'
        |     |     |     |  \___attribute 'parentSI' = 'kilogramsPerSquareMeter'
        |     |     |     |  \___attribute 'unitType' = 'arealMassDensity'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.1' ('stmml:description')
        |     |     |     |     |___text 'milligrams Per Square Meter'
        |     |     |     |___text '\n        '
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Copyright 2024 Environmental Data Initiative. This material is based upon work supported by the National Science Foundation under grants #2223103 and #2223104. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Please contact us with questions, comments, or for technical assistance regarding this web site or the Environmental Data Initiative. Please read our privacy policy to know what information we collect about you and to understand your privacy rights.

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

Data Package Metadata View Summary

Benthic algae chlorophyll measurements for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.

Data Entities

Data Table

Non-Categorized Data Resource

Data Package Usage Rights

Data Policies

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

Maintenance

Additional Metadata

Recently Added

Recently Updated

Data Package Metadata View Summary

Benthic algae chlorophyll measurements for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.

+/- Data Entities

Data Table

Non-Categorized Data Resource

+/- Data Package Usage Rights

Data Policies

+/- 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

+/- 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