http://lod.bco-dmo.org/id/dataset/738142
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2018-06-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Isotopic composition of phospholipid-linked fatty acids (PLFAs) in the surface sediments of three marsh ponds in PIE-LTER (Rowley, MA) from 2014.
2018-06-05
publication
2018-06-05
revision
BCO-DMO Linked Data URI
2018-06-05
creation
http://lod.bco-dmo.org/id/dataset/738142
Amanda Spivak
Woods Hole Oceanographic Institution
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Spivak, A. (2018) Isotopic composition of phospholipid-linked fatty acids (PLFAs) in the surface sediments of three marsh ponds in PIE-LTER (Rowley, MA) from 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-06-05 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/738142 [access date]
Isotopic composition of phospholipid-linked fatty acids (PLFAs) in the surface sediments of three marsh ponds in PIE-LTER (Rowley, MA). Data were collected over 11 weeks in the summer and fall of 2014. Dataset Description: <p>Isotopic composition of phospholipid-linked fatty acids (PLFAs) in the surface sediments of three marsh ponds in PIE-LTER (Rowley, MA). Data were collected over 11 weeks in the summer and fall of 2014.</p> Methods and Sampling: <p>The three ponds are located in the high marsh (1.43-1.46 m above North American Vertical Datum of 1988) of the Plum Island Ecosystems – Long Term Ecological Research (PIE-LTER) site. Surface sediments were collected weekly June 25-August 13 and November 11-25, 2014. Cores (5 cm diameter x 2 cm deep) were collected from three 1 m<sup>2</sup> quadrats placed at random locations along two crisscrossing transects in each pond. Sediments were combined in combusted glass vials to form composite samples and stored (-80 ℃) until analysis. Lipid biomarker compounds were extracted using a modified Bligh &amp; Dyer (1959) method (Spivak and Reeve 2015). Sediments were extracted with a methanol : chloroform : phosphate buffer saline mixture (2:1:0.8, v:v:v) using a microwave-accelerated reaction system (MARS6); samples were heated to 80°C for 10 min with continuous stirring. Samples were then partitioned and the organic phase removed. The total lipid extract was concentrated under N<sub>2</sub> and samples were eluted on silica gel columns with chloroform, acetone (F1/2), and methanol (F3) (Guckert et al. 1985). The F3 (phospholipids) was dried under N<sub>2</sub> and saponified with 0.5 M NaOH at 70°C for 4 h. Saponified samples were acidified and extracted 3 times with hexane. The extract was methylated with acidic methanol (95:5 methanol:HCl) and heated overnight at 70°C to form fatty acid methyl esters (FAME). Samples were analyzed with an Agilent 7890 gas chromatograph with the effluent split ~70:30 between a 5975C mass spectrometer and a flame ionization detector. Compounds were separated on an Agilent DB-5 ms column (60 m, 0.25 mm inner diameter, 0.25 μm film). FAME concentrations were quantified using methyl heneicosanoate as an internal standard. FAs are designated A:BωC, where A is the number of carbon atoms, B is the number of double bonds, and C is the position of the first double bond from the aliphatic ‘<em>ω</em>’ end of the molecule. Iso- and anteiso refer to whether the methyl group of branched compounds is attached to the penultimate or antepenultimate carbon atom. Stable carbon isotope ratios of FAMEs were determined by the WHOI Organic Mass Spectrometry Facility with a Hewlett-Packard 6890 GC coupled to a DeltaPlus isotope-ratio-monitoring gas chromatography-mass spectrometer (IRM-GCMS) via a GCCIII combustion interface held at 850 °C with a constant oxygen trickle. Isotopic values of phospholipid-linked fatty acids (PLFAs) were derived from the isotopic composition of FAMEs and corrected for the δ<sup>13</sup>C of the carbon added during methylation using a mass balance approach as well as for a -3‰ fractionation during lipid synthesis (Bouillon and Boschker 2006; Hayes 2001). The δ<sup>13</sup>C of PLFA subclasses was calculated as concentration weighted averages (Spivak and Ossolinski 2016).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1233678 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1233678
completed
Amanda Spivak
Woods Hole Oceanographic Institution
706-542-5709
Marine Science Rm. 164 Department of Marine Science
Athens
GA
30602
United States
aspivak@uga.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Season
Tide
Week
Pond
BrFA
Methyl_10_C16
C18_1
C18_2
PUFA
C18_4
C18_2_2
Agilent 7890 gas chromatograph
Hewlett-Packard 6890 GC
5975C mass spectrometer
DeltaPlus isotope-ratio-monitoring gas chromatography-mass spectrometer (IRM-GCMS)
Corer
theme
None, User defined
season
No BCO-DMO term
time_point
Site_ID
featureType
BCO-DMO Standard Parameters
Gas Chromatograph
Gas Chromatograph
Isotope-ratio Mass Spectrometer
Isotope-ratio Mass Spectrometer
Push Corer
instrument
BCO-DMO Standard Instruments
Plum_Island
service
Deployment Activity
Plumn Island, MA
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Eutrophication Effects on Sediment Metabolism and Benthic Algal-bacterial Coupling: An Application of Novel Techniques in a LTER Estuary
https://osprey.bco-dmo.org/project/529583
Eutrophication Effects on Sediment Metabolism and Benthic Algal-bacterial Coupling: An Application of Novel Techniques in a LTER Estuary
<p><em>Extracted from the NSF award abstract:</em><br />
This project will address how rates of benthic microalgal production respond to eutrophication and geomorphological changes in human-impacted tidal creeks. Excess nutrient loading increases benthic algal biomass and likely stimulates production rates but the magnitude of nutrient and geomorphological effects on rates of production is unknown. Will changes in benthic algal productivity affect algal-bacterial coupling? Furthermore, how is algal-bacterial coupling affected by geomorphological changes, which may be exacerbated by excess nutrient loading but can also occur in pristine marshes?</p>
<p>This project will take advantage of the infrastructure of the TIDE project, a long-term saltmarsh eutrophication experiment at the Plum Island Ecosystem - Long Term Ecological Research site in Northeastern Massachusetts. Specifically, the PIs will measure benthic metabolism and examine algal- bacterial coupling in fertilized and ambient nutrient tidal creeks in the first field season. The following field season, they will compare sediment metabolism and carbon dynamics on slumped tidal creek walls (i.e. areas where low marsh has collapsed into the tidal creek) to that on the bottom of tidal creeks. In both years, gross and net production will be determined using an innovative triple oxygen isotope technique and traditional dissolved oxygen and inorganic carbon flux measurements. Comparisons between these methods will be useful in informing studies of sediment metabolism. Lipid biomarkers will be used to characterize the sources of organic matter to creek sediments, and stable isotope analysis of bacterial specific biomarkers to identify the sources of organic carbon utilized by sediment bacteria. The biomarkers will reveal whether sediment bacteria use organic matter substrates, such as benthic microalgal carbon, selectively or in proportion to availability. Overall, results from the proposed study will provide important information about how sediment carbon dynamics in shallow tidal creeks respond to long term eutrophication. Furthermore, findings will enhance understanding of the role of tidal creeks in coastal biogeochemistry.</p>
Benthic_PP_at_TIDE
largerWorkCitation
project
eng; USA
oceans
Plumn Island, MA
-70.809432
-70.809432
42.738349
42.738349
2014-09-01
2014-11-30
Plum Island Estuary, Rowley Massachusetts
0
BCO-DMO catalogue of parameters from Isotopic composition of phospholipid-linked fatty acids (PLFAs) in the surface sediments of three marsh ponds in PIE-LTER (Rowley, MA) from 2014.
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/738410.rdf
Name: Season
Units: unitless
Description: <p>Season at time of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/738411.rdf
Name: Tide
Units: unitless
Description: <p>Tide type</p>
http://lod.bco-dmo.org/id/dataset-parameter/738412.rdf
Name: Week
Units: unitless
Description: <p>Week number</p>
http://lod.bco-dmo.org/id/dataset-parameter/738413.rdf
Name: Pond
Units: unitless
Description: <p>Site number</p>
http://lod.bco-dmo.org/id/dataset-parameter/738414.rdf
Name: BrFA
Units: per mil
Description: <p>Branched fatty acids; sum iso- anteiso (C13, C15, C17)</p>
http://lod.bco-dmo.org/id/dataset-parameter/738415.rdf
Name: Methyl_10_C16
Units: per mil
Description: <p>Concentration 10 methyl C16</p>
http://lod.bco-dmo.org/id/dataset-parameter/738416.rdf
Name: C18_1
Units: per mil
Description: <p>Concentration C18 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/738417.rdf
Name: C18_2
Units: per mil
Description: <p>Concentration C18 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/738418.rdf
Name: PUFA
Units: per mil
Description: <p>Polyunsaturated fatty acids; sum(C20:4, C20:5, C22:5, C22:6)</p>
http://lod.bco-dmo.org/id/dataset-parameter/738419.rdf
Name: C18_4
Units: per mil
Description: <p>Concentration C18 4</p>
http://lod.bco-dmo.org/id/dataset-parameter/738420.rdf
Name: C18_2_2
Units: per mil
Description: <p>Concentration C18 2</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
1606
https://datadocs.bco-dmo.org/file/R88XmPxUvGpAG5/PLFA_CSIA.csv
PLFA_CSIA.csv
Primary data file for dataset ID 738142
download
https://osprey.bco-dmo.org/dataset/738142/data/download
download
onLine
dataset
<p>The three ponds are located in the high marsh (1.43-1.46 m above North American Vertical Datum of 1988) of the Plum Island Ecosystems – Long Term Ecological Research (PIE-LTER) site. Surface sediments were collected weekly June 25-August 13 and November 11-25, 2014. Cores (5 cm diameter x 2 cm deep) were collected from three 1 m<sup>2</sup> quadrats placed at random locations along two crisscrossing transects in each pond. Sediments were combined in combusted glass vials to form composite samples and stored (-80 ℃) until analysis. Lipid biomarker compounds were extracted using a modified Bligh &amp; Dyer (1959) method (Spivak and Reeve 2015). Sediments were extracted with a methanol : chloroform : phosphate buffer saline mixture (2:1:0.8, v:v:v) using a microwave-accelerated reaction system (MARS6); samples were heated to 80°C for 10 min with continuous stirring. Samples were then partitioned and the organic phase removed. The total lipid extract was concentrated under N<sub>2</sub> and samples were eluted on silica gel columns with chloroform, acetone (F1/2), and methanol (F3) (Guckert et al. 1985). The F3 (phospholipids) was dried under N<sub>2</sub> and saponified with 0.5 M NaOH at 70°C for 4 h. Saponified samples were acidified and extracted 3 times with hexane. The extract was methylated with acidic methanol (95:5 methanol:HCl) and heated overnight at 70°C to form fatty acid methyl esters (FAME). Samples were analyzed with an Agilent 7890 gas chromatograph with the effluent split ~70:30 between a 5975C mass spectrometer and a flame ionization detector. Compounds were separated on an Agilent DB-5 ms column (60 m, 0.25 mm inner diameter, 0.25 μm film). FAME concentrations were quantified using methyl heneicosanoate as an internal standard. FAs are designated A:BωC, where A is the number of carbon atoms, B is the number of double bonds, and C is the position of the first double bond from the aliphatic ‘<em>ω</em>’ end of the molecule. Iso- and anteiso refer to whether the methyl group of branched compounds is attached to the penultimate or antepenultimate carbon atom. Stable carbon isotope ratios of FAMEs were determined by the WHOI Organic Mass Spectrometry Facility with a Hewlett-Packard 6890 GC coupled to a DeltaPlus isotope-ratio-monitoring gas chromatography-mass spectrometer (IRM-GCMS) via a GCCIII combustion interface held at 850 °C with a constant oxygen trickle. Isotopic values of phospholipid-linked fatty acids (PLFAs) were derived from the isotopic composition of FAMEs and corrected for the δ<sup>13</sup>C of the carbon added during methylation using a mass balance approach as well as for a -3‰ fractionation during lipid synthesis (Bouillon and Boschker 2006; Hayes 2001). The δ<sup>13</sup>C of PLFA subclasses was calculated as concentration weighted averages (Spivak and Ossolinski 2016).</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Data Processing Notes:</strong></p>
<p>-reformatted column names to comply with BCO-DMO standards<br />
-filled in blank cells with "nd"</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Agilent 7890 gas chromatograph
Agilent 7890 gas chromatograph
PI Supplied Instrument Name: Agilent 7890 gas chromatograph PI Supplied Instrument Description:Used to analyze samples Instrument Name: Gas Chromatograph Instrument Short Name:Gas Chromatograph Instrument Description: Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB02/
Hewlett-Packard 6890 GC
Hewlett-Packard 6890 GC
PI Supplied Instrument Name: Hewlett-Packard 6890 GC PI Supplied Instrument Description:Used to determine stable carbon isotope ratios of FAMEs Instrument Name: Gas Chromatograph Instrument Short Name:Gas Chromatograph Instrument Description: Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB02/
5975C mass spectrometer
5975C mass spectrometer
PI Supplied Instrument Name: 5975C mass spectrometer PI Supplied Instrument Description:Extracted and analyzed samples Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec; IRMS Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
DeltaPlus isotope-ratio-monitoring gas chromatography-mass spectrometer (IRM-GCMS)
DeltaPlus isotope-ratio-monitoring gas chromatography-mass spectrometer (IRM-GCMS)
PI Supplied Instrument Name: DeltaPlus isotope-ratio-monitoring gas chromatography-mass spectrometer (IRM-GCMS) PI Supplied Instrument Description:Used to determine stable carbon isotope ratios of FAMEs Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec; IRMS Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Corer
Corer
PI Supplied Instrument Name: Corer PI Supplied Instrument Description:Used to collect sediment samples Instrument Name: Push Corer Instrument Short Name: Instrument Description: Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.
Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/
Deployment: Plum_Island
Plum_Island
shoreside Massachusetts
shoreside
Plum_Island
Rachel H. R. Stanley
Wellesley College
shoreside Massachusetts
shoreside