Data Package Metadata View Summary

Biogeochemical rate data and sediment properties of samples used for a controlled flow through experiment testing the effect of nitrate on organic matter decomposition, PIE LTER, Plum Island Sound estuary, Massachusetts.

General Information

Data Package:
Local Identifier:	knb-lter-pie.538.1
Title:	Biogeochemical rate data and sediment properties of samples used for a controlled flow through experiment testing the effect of nitrate on organic matter decomposition, PIE LTER, Plum Island Sound estuary, Massachusetts.
Alternate Identifier:	DOI PLACE HOLDER
Abstract:	In this dataset, we used a controlled flow-through reactor (FTR) experiment to test the role of nitrate as an electron acceptor, and its effect on organic matter decomposition and the associated microbial community in salt marsh sediments. Organic matter decomposition significantly increased in response to nitrate, even at sediment depths typically considered resistant to decomposition. The use of isotope tracers suggests this pattern was largely driven by stimulated denitrification. Nitrate addition also significantly altered the microbial community and decreased alpha diversity, selecting for taxa belonging to groups known to reduce nitrate and oxidize more complex forms of organic matter. Fourier Transform-Infrared Spectroscopy further supported these results, suggesting that nitrate facilitated decomposition of complex organic matter compounds into more bioavailable forms. Taken together, these results suggest the existence of organic matter pools that only become accessible with nitrate and would otherwise remain stabilized in the sediment. The existence of such pools could have important implications for carbon storage, since greater decomposition rates as N loading increases may result in less overall burial of organic-rich sediment. Given the extent of nitrogen loading along our coastlines, it is imperative that we better understand the resilience of salt marsh systems to nutrient enrichment, especially if we hope to rely on salt marshes, and other blue carbon systems, for long-term carbon storage.
Short Name:	STP-MAR-Nitrate-FlowReactorExpt
Publication Date:	2019
Language:	English

Time Period

Begin:

2015-12-16

End:

2016-03-12

People and Organizations
Contact:	Plum Island Ecosystems LTER
Creator:	Bulseco-McKim, Ashley
Creator:	Giblin, Anne
Creator:	Bowen, Jennifer
Associate:	Tucker, Jane
Associate:	Vallino, Joe
Associate:	Murphy, Anna
Associate:	Sanderman, Jonathan
Associate:	Hiller-Bittrolf, Kenly

Data Entities
Data Table Name:	STP-MAR-Nitrate-FlowReactorExpt_csv
Description:	Biogeochemical rate data and sediment properties of samples used for a controlled flow through experiment testing the effect of nitrate on organic matter decomposition, PIE LTER, Plum Island Sound estuary, Massachusetts.
Other Name:	STP-MAR-Nitrate-FlowReactorExpt_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/538/1/0360c1487252686ae7fc0d30eb7560d1
Name:	STP-MAR-Nitrate-FlowReactorExpt_csv
Description:	Biogeochemical rate data and sediment properties of samples used for a controlled flow through experiment testing the effect of nitrate on organic matter decomposition, PIE LTER, Plum Island Sound estuary, Massachusetts.
Number of Records:	27
Number of Columns:	21

Table Structure

Object Name:

STP-MAR-Nitrate-FlowReactorExpt.csv

Size:

3276

Authentication:

6c7f72719bad039bf3ed86654eb46e15 Calculated By MD5

Authentication:

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Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:

Table Column Descriptions

ExptDate

SampleID

Treatment

Depth

Core

DIC

Nitrate

DNF

Ammonium

Sulfide

SRR

BulkDensity

DryWetRatio

PercOM

PercSulfur

WetWeight

WaterContent

PercNitrogen

PercCarbon

MolarCN

AlphaDiversity

Column Name:

ExptDate

SampleID

Treatment

Depth

Core

DIC

Nitrate

DNF

Ammonium

Sulfide

SRR

BulkDensity

DryWetRatio

PercOM

PercSulfur

WetWeight

WaterContent

PercNitrogen

PercCarbon

MolarCN

AlphaDiversity

Definition:

Experiment start date

Sample Identifier (Format: Treatment:Core:Depth)

Treatment

Sediment depth

Core number

DIC production integrated over time

Total nitrate reduction integrated over time

Total DNF production (from N2 production)

Total ammonium production integrated over time

Total sulfide production integrated over time

Total sulfate reduction (sulfide production + total sulfur) integrated over time

Bulk density (grams dry weight/volume). Used dry-to-wet ratio from breakdown masses

Ratio of dry-to-wet sediment mass used for bulk density calculation

Percent organic matter from loss-on-ignition (550 deg C for three hours)

Change in % sulfur

Sediment mass at breakdown per reactor

Difference between dry and wet weight

%N in sample analyzed on a Costech EA at UMB

%C in sample analyzed on a Costech EA at UMB

Molar C:N ratio calculated from %N and %C

Shannon diversity of microbial communities

Storage Type:

date

string

Measurement Type:

dateTime

nominal

ratio

Measurement Values Domain:

Format	YYYY-MM-DD
Precision

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	N
Definition	nitrate
Source

Code Definition

Code	S
Definition	shallow
Source

Code Definition

Code	1
Definition	core 1 replicate
Source

Code Definition

Code	2
Definition	core 2 replicate
Source

Code Definition

Code	3
Definition	core 3 replicate
Source

Code Definition

Code	M
Definition	Mid
Source

Code Definition

Code	D
Definition	deep
Source

Definition

Treatment

Definition

Sediment depth

Unit	number
Type	real

Unit	micromolePerCentimeterCubed
Type	real

Unit	micromolePerCentimeterCubed
Type	real

Unit	micromolePerCentimeterCubed
Type	real

Unit	micromolePerCentimeterCubed
Type	real

Unit	micromolePerCentimeterCubed
Type	real

Unit	micromolePerCentimeterCubed
Type	real

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Unit	percent
Type	real

Unit	percent
Type	real

Unit	gram
Type	real

Unit	gram
Type	real

Unit	percent
Type	real

Unit	percent
Type	real

Unit	dimensionless
Type	real

Unit	dimensionless
Type	real

Missing Value Code:

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Code	NA
Expl	not available

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Non-Categorized Data Resource

Name:

STP-MAR-Nitrate-FlowReactorExpt_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:

STP-MAR-Nitrate-FlowReactorExpt.xls

Size:

110592

Authentication:

ab8e250ad4cf753a193afd4f74f65009 Calculated By MD5

Authentication:

bceb7e4742f5542f0b2f5f1666edcd14e9c36a15 Calculated By SHA-1

Externally Defined Format:

Format Name:

application/vnd.ms-excel

Data:

https://pasta-s.lternet.edu/package/data/eml/knb-lter-pie/538/1/9720c8c62e233c53bafc372f5ff353cb

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	Organic Matter, Inorganic Nutrients, Population Dynamics
LTER Controlled Vocabulary	genetics, community dynamics, population dynamics, salt marshes, carbon, nitrogen, nitrate, nitrate, sulfur, sulfate, soil organic matter, sediments, carbon fluxes, diversity, bacteria, PIE LTER, Plum Island Ecosystems, decomposition, nitrogen mineralization, nitrogen mineralization, sediment

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:

The FTR experimental design is a modified version of a system described in Pallud &amp; Van Cappellen (2006). We collected sediment cores (n=3; 5 cm diameter and 30 cm deep) from tall Spartina alterniflora approximately 1 meter from the creek bank edge, in West Creek (42.759N, 70.891 W). We sectioned each core into shallow (0-5 cm), mid (10-15 cm), and deep (20-25 cm) sediments and homogenized sections under anoxic conditions, and split each depth section into two treatments -- nitrate (+500 uM labeled potassium nitrate in 0.2um filtered seawater) and unamended (0.2 um filtered seawater only). These sediments were loaded into the FTRs, with an approximate volume of 31.81 cm^3. The reactors received constant flow of one of the two treatments mentioned above using peristaltic pumps flowing at ~0.08 mL/min, under anoxic conditions. We collected outflow samples to assess biogeochemical parameters, and collected sediment at the beginning and end of the experiment to assess the microbial community and sediment carbon parameters. More information regarding the experimental design can be found in Bulseco et al. 2019.
We measured the following biogeochemical parameters using the associated methods: dissolved inorganic carbon using an Apollo SciTech AS-C3 DIC Analyzer (Dickson &amp; Goyet 1994); nitrate + nitrite using chemiluminescence on a Teledyne T200 NOx analyzer (Cox 1980); ammonium on a Shimadzu 1601 spectrophotometer (Solorzano 1969); sulfide on a Shimadzu 1601 spectrophotometer (Gilboa-Garber 1971); denitrification and DNRA by measuring production of 28, 29, and 30N2 on a membrane inlet mass spectrometer (Kana et al. 1994; Yin et al. 2014); %C and %N on a Perkin Elmer 2400 Series Elemental Analyzer; %sulfur on a LECO S635S sulfur analyzer; sediment functional groups on a Fourier Transform-Infrared Spectrometer (Margenot et al. 2015).
We performed molecular work using the following procedures. We extracted DNA using the MoBio PowerSoil DNA Isolation Kit; amplified the V4 region of the 16S rRNA gene using the general bacterial primer pair 515F/806R (Caporaso et al. 2011) on an Illumia MiSeq (Caporaso et al. 2012) using a 300-cycle kit and V2 chemistry. Sequence analysis was conducted in QIIME2, version 2017.12) and statistical analyses were completed using R (R Core Team 2013). Microbial genomic sequence data from this study is available in the Sequence Read Archive under accession number PRJNA505917.

People and Organizations

Publishers:

Organization:

Plum Island Ecosystems LTER

Web Address:

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

Creators:

Individual:

Ashley Bulseco-McKim

Address:

Northeastern University, Marine Science Center,

Nahant, MA Nahant US

Email Address:

bulseco.a@husky.neu.edu

Individual:

Anne Giblin

Address:

Marine Biological Lab, 7 MBL Street,

Woods Hole, MA 02543 US

Phone:

(508) 289-7488 (voice)

Phone:

(508) 457-1548 (facsimile)

Email Address:

agiblin@mbl.edu

Id:

http://orcid.org/0000-0003-3851-2178

Individual:

Jennifer Bowen

Address:

Northeastern University, Marine Science Center, 430 Nahant Road,

Nahant, MA 01908 US

Phone:

(781) 581-7370 x346 (voice)

Email Address:

je.bowen@northeastern.edu

Contacts:

Organization:

Plum Island Ecosystems LTER

Web Address:

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

Associated Parties:

Individual:

Jane Tucker

Address:

Marine Biological Lab, 7 MBL Street,

Woods Hole, MA 02543 US

Phone:

(508) 289-7469 (voice)

Email Address:

jtucker@mbl.edu

Id:

https://orcid.org/0000-0002-9119-8539

Role:

associated researcher

Individual:

Joe Vallino

Address:

Marine Biological Laboratory, 7 MBL Street,

Woods Hole, MA 02543 US

Phone:

(508) 289-7648 (voice)

Phone:

(508) 457-1548 (facsimile)

Email Address:

jvallino@mbl.edu

Id:

http://orcid.org/0000-0002-4184-4512

Role:

associated researcher

Individual:

Anna Murphy

Address:

Department of Marine and Environmental Science, Northeastern University,

Nahant, MA 01908 US

Role:

associated researcher

Individual:

Jonathan Sanderman

Address:

Woods Hole Research Center,

Falmouth, MA 02540 US

Role:

associated researcher

Individual:

Kenly Hiller-Bittrolf

Address:

Department of Biology, University of Massachusetts Boston,

Boston, MA 02125 US

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:

2015-12-16

End:

2016-03-12

Sampling Site:

Description:

West Creek, off Rowley River, Rowley, MA.

Site Coordinates:

Longitude (degree):

-70.849662780762

Latitude (degree):

42.737945556641

Project

Parent Project Information:

Title:

Plum Island Ecosystems Long Term Ecological Research (PIE LTER IV, 2016-2022)

Personnel:

Individual:

Anne Giblin

Address:

Marine Biological Lab, 7 MBL Street,

Woods Hole, MA 02543 US

Phone:

(508) 289-7488 (voice)

Phone:

(508) 457-1548 (facsimile)

Email Address:

agiblin@mbl.edu

Id:

http://orcid.org/0000-0003-3851-2178

Role:

principalInvestigator

Individual:

Wilfred Wollheim

Address:

WSAG Institute for the Study of Earth, Oceans, and Space,Morse Hall, Room 452, 8 College Road,

Durham, NH 03824 US

Phone:

(603) 862-0812 (voice)

Email Address:

Wil.Wollheim@unh.edu

Id:

http://orcid.org/0000-0002-5009-3212

Role:

principalInvestigator

Individual:

Jim Morris

Address:

Bell Baruch Institute for Marine and Coastal Sciences, University of South Carolina,

Columbia, SC 29208 US

Phone:

(803) 777-5288 (voice)

Phone:

(803) 777-4002 (facsimile)

Email Address:

morris@inlet.geol.sc.edu

Role:

principalInvestigator

Individual:

Nathaniel Weston

Address:

Department of Geography and the Environment ,Villanova University, 800 Lancaster Avenue,

Villanova, PA 19085 US

Phone:

(610) 519-8009 (voice)

Email Address:

nathaniel.weston@villanova.edu

Id:

http://orcid.org/0000-0002-6837-360X

Role:

principalInvestigator

Individual:

Linda Deegan

Address:

Woods Hole Research Center,

Falmouth, MA 02540 US

Phone:

508-444-1557 (voice)

Email Address:

ldeegan@whrc.org

Id:

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

Role:

principalInvestigator

Individual:

Joe Vallino

Address:

Marine Biological Laboratory, 7 MBL Street,

Woods Hole, MA 02543 US

Phone:

(508) 289-7648 (voice)

Phone:

(508) 457-1548 (facsimile)

Email Address:

jvallino@mbl.edu

Id:

http://orcid.org/0000-0002-4184-4512

Role:

principalInvestigator

Individual:

Robert Pontius

Address:

Clark University, School of Geography, 950 Main Street,

Worcester, MA 01610 US

Phone:

(508) 793-7761 (voice)

Phone:

(508) 793-8881 (facsimile)

Email Address:

rpontius@clarku.edu

Id:

http://orcid.org/0000-0001-7287-5875

Role:

principalInvestigator

Individual:

Jarrett Byrnes

Address:

University of Massachusetts, College of Science and Mathematics,100 Morrissey Blvd,

Boston, MA 02125 US

Phone:

(617) 287-3145 (voice)

Email Address:

Jarrett.Byrnes@umb.edu

Id:

http://orcid.org/0000-0002-9791-9472

Role:

principalInvestigator

Abstract:

The Plum Island Ecosystems (PIE) LTER is developing a predictive understanding of the response of a linked watershed-marsh-estuarine system in northeastern Massachusetts to rapid environmental change. Over the last 30 years, surface sea water temperatures in the adjacent Gulf of Maine have risen at 3 times the global average, rates of sea-level rise have accelerated, and precipitation has increased. Coupled with these changes in climate and sea level are substantial changes within the rapidly urbanizing watersheds that influence water, sediment, and nutrient delivery to the marsh and estuary. In PIE IV our focus is on: Dynamics of coastal ecosystems in a region of rapid climate change, sea-level rise, and human impacts.

NSF OCE LTER-Plum Island Ecosystems:
Dynamics of coastal ecosystems in a region of rapid climate change, sea-level rise, and human impacts.

Funding:

1637630

Maintenance

Maintenance:

Description:

Experiment complete.
Version 01: September 11, 2019, data and metadata updates to comply with importation to DEIMS7 and LTER Data Portal. Used MarcrosExportEML_HTML (working)pie_excel2007_Sep2019.xlsm 9/3/19 5:19 PM for QA/QC to EML 2.1.0

Frequency:

Other Metadata

Additional Metadata

additionalMetadata
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        |     |     |___text '\n        '
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        |     |     |     |  \___attribute 'abbreviation' = 'umole/cm3'
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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.

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Data Package Metadata View Summary

Biogeochemical rate data and sediment properties of samples used for a controlled flow through experiment testing the effect of nitrate on organic matter decomposition, PIE LTER, Plum Island Sound estuary, Massachusetts.

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

Parent Project Information:

Maintenance

Additional Metadata

Recently Added

Recently Updated

Data Package Metadata View Summary

Biogeochemical rate data and sediment properties of samples used for a controlled flow through experiment testing the effect of nitrate on organic matter decomposition, PIE LTER, Plum Island Sound estuary, Massachusetts.

+/- 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

Parent Project Information:

+/- Maintenance

+/- Additional Metadata

Data Entities

Data Package Usage Rights

Keywords

Methods and Protocols

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Maintenance

Additional Metadata