Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | Raw concentrations of individual PLFA compounds from Massachusetts from 2012- 2015. 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_669693) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Data Access Form
| Files
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![[The graph you specified. Please be patient.]](https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_669693.png?month,c12&.draw=markers&.marker=5%7C5&.color=0x000000&.colorBar=%7C%7C%7C%7C%7C&.bgColor=0xffccccff)
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Attributes {
s {
month {
Byte _FillValue 127;
Byte actual_range 6, 10;
String bcodmo_name "month";
String description "Month samples were collected; mm";
String long_name "Month";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/MNTHXXXX/";
String units "unitless";
}
estuary {
String bcodmo_name "site";
String description "The core originiated from Sweeny or West tidal creeks";
String long_name "Estuary";
String units "unitless";
}
timepoint {
String bcodmo_name "time";
String description "Timepoint refers to when the sample was collected before (PL) or after the 13C-isotope label was added; HH:MM";
String long_name "Timepoint";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/";
String units "unitless";
}
experiment {
String bcodmo_name "treatment";
String description "Experiment refers to whether the 13C label was applied as benthic microalgae (BMA) or Spartina alterniflora (salt) detritus.";
String long_name "Experiment";
String units "unitless";
}
c12 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 206.1128748;
String bcodmo_name "unknown";
String description "Concentration of a combination of algae and microbes; short chain fatty acid";
String long_name "C12";
String units "percentage";
}
i13 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 150.2383931;
String bcodmo_name "unknown";
String description "iso methyl branced FA; indicates whether the methyl group is attached to the penultimate carbon atom";
String long_name "I13";
String units "percentage";
}
a13 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 91.09708692;
String bcodmo_name "unknown";
String description "anteiso methyl branced FAs; indicates whether methyl group is attached to the antepenultimate carbon atom";
String long_name "A13";
String units "percentage";
}
c13 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 119.9632599;
String bcodmo_name "unknown";
String description "Concentration of a combination of algae and microbes; short chain fatty acid";
String long_name "C13";
String units "percentage";
}
i14 {
Float64 _FillValue NaN;
Float64 actual_range 35.46011518, 671.5094428;
String bcodmo_name "unknown";
String description "iso methyl branced FA; indicates whether the methyl group is attached to the penultimate carbon atom";
String long_name "I14";
String units "percentage";
}
c14 {
Float64 _FillValue NaN;
Float64 actual_range 167.6936885, 3028.253378;
String bcodmo_name "unknown";
String description "Conentration of carbon isotope";
String long_name "C14";
String units "percentage";
}
i15 {
Float64 _FillValue NaN;
Float64 actual_range 195.4219156, 3246.9206;
String bcodmo_name "unknown";
String description "iso methyl branced FA; indicates whether the methyl group is attached to the penultimate carbon atom";
String long_name "I15";
String units "percentage";
}
a15 {
Float64 _FillValue NaN;
Float64 actual_range 231.4117033, 3405.412976;
String bcodmo_name "unknown";
String description "anteiso methyl branced FAs; indicates whether methyl group is attached to the antepenultimate carbon atom";
String long_name "A15";
String units "percentage";
}
c15 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 2286.475985;
String bcodmo_name "unknown";
String description "Concentration of carbon isotope";
String long_name "C15";
String units "percentage";
}
i16 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 1391.526599;
String bcodmo_name "unknown";
String description "iso methyl branced FA; indicates whether the methyl group is attached to the penultimate carbon atom";
String long_name "I16";
String units "percentage";
}
c16 {
Float64 _FillValue NaN;
Float64 actual_range 1186.110944, 18218.21615;
String bcodmo_name "unknown";
String description "Concentration of sulfate reducing bacteria";
String long_name "C16";
String units "percentage";
}
me10_16 {
Float64 _FillValue NaN;
Float64 actual_range 43.08731042, 1393.518209;
String bcodmo_name "unknown";
String description "Concentration of sulfate reducing bacteria";
String long_name "Me10 16";
String units "percentage";
}
i17 {
Float64 _FillValue NaN;
Float64 actual_range 110.6613021, 1341.707896;
String bcodmo_name "unknown";
String description "iso methyl branced FA; indicates whether the methyl group is attached to the penultimate carbon atom";
String long_name "I17";
String units "percentage";
}
a17 {
Float64 _FillValue NaN;
Float64 actual_range 100.0341077, 1211.512171;
String bcodmo_name "unknown";
String description "anteiso methyl branced FAs; indicates whether methyl group is attached to the antepenultimate carbon atom";
String long_name "A17";
String units "percentage";
}
c17 {
Float64 _FillValue NaN;
Float64 actual_range 66.46104389, 1864.874336;
String bcodmo_name "unknown";
String description "Concentration of carbon isotope";
String long_name "C17";
String units "percentage";
}
c18 {
Float64 _FillValue NaN;
Float64 actual_range 351.4167529, 5907.906658;
String bcodmo_name "unknown";
String description "Concentration of carbon isotope";
String long_name "C18";
String units "percentage";
}
i19 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 361.1033459;
String bcodmo_name "unknown";
String description "iso methyl branced FA; indicates whether the methyl group is attached to the penultimate carbon atom";
String long_name "I19";
String units "percentage";
}
a19 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 426.0938027;
String bcodmo_name "unknown";
String description "anteiso methyl branced FAs; indicates whether methyl group is attached to the antepenultimate carbon atom";
String long_name "A19";
String units "percentage";
}
c19 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 720.9545328;
String bcodmo_name "unknown";
String description "Concentration of carbon isotope";
String long_name "C19";
String units "percentage";
}
c20_5w3 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 4058.707755;
String bcodmo_name "unknown";
String description "Isotopic composition of compounds and subclasses representing algae; polyunsaturated fatty acids";
String long_name "C20 5W3";
String units "percentage";
}
c20_4w6 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 13707.70829;
String bcodmo_name "unknown";
String description "Isotopic composition of compounds and subclasses representing algae; polyunsaturated fatty acids";
String long_name "C20 4W6";
String units "percentage";
}
c20 {
Float64 _FillValue NaN;
Float64 actual_range 114.9411689, 1222.542132;
String bcodmo_name "unknown";
String description "Concentration of carbon isotope";
String long_name "C20";
String units "percentage";
}
c21 {
Float64 _FillValue NaN;
Float64 actual_range 192.4533648, 1665.933443;
String bcodmo_name "unknown";
String description "Concentration of carbon isotope";
String long_name "C21";
String units "percentage";
}
unsatC22 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 588.9289876;
String bcodmo_name "unknown";
String description "Concentration of unsaturated fatty acids";
String long_name "Unsat C22";
String units "percentage";
}
c22_6w3 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 5314.589072;
String bcodmo_name "unknown";
String description "Isotopic composition of compounds and subclasses representing algae; polyunsaturated fatty acids";
String long_name "C22 6W3";
String units "percentage";
}
c22_5 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 1949.542406;
String bcodmo_name "unknown";
String description "Isotopic composition of compounds and subclasses representing algae; polyunsaturated fatty acids";
String long_name "C22 5";
String units "percentage";
}
c22 {
Float64 _FillValue NaN;
Float64 actual_range 106.8008664, 669.3160305;
String bcodmo_name "unknown";
String description "Concentration of carbon isotope";
String long_name "C22";
String units "percentage";
}
c23 {
Float64 _FillValue NaN;
Float64 actual_range 270.0952806, 2098.195845;
String bcodmo_name "unknown";
String description "Concentration of carbon isotope";
String long_name "C23";
String units "percentage";
}
c24 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 2055.123381;
String bcodmo_name "unknown";
String description "Concentration of carbon isotope";
String long_name "C24";
String units "percentage";
}
c26 {
Float64 _FillValue NaN;
Float64 actual_range 121.8191041, 2053.79792;
String bcodmo_name "unknown";
String description "Concentration of carbon isotope";
String long_name "C26";
String units "percentage";
}
c28 {
Float64 _FillValue NaN;
Float64 actual_range 0.0, 1671.278298;
String bcodmo_name "unknown";
String description "Concentration of carbon isotope";
String long_name "C28";
String units "percentage";
}
totalFA {
Float64 _FillValue NaN;
Float64 actual_range 4211.561565, 65874.63067;
String bcodmo_name "unknown";
String description "Total fatty acid concentration";
String long_name "Total FA";
String units "percentage";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Methodology from\\u00a0Spivak, AC and J Ossolinski. 2016. Limited effects of
nutrient enrichment on bacterial carbon sources in salt marsh tidal creek
sediments. Marine Ecology Progress Series. 544:107-130. 10.3354/meps11587
In June, August, and October 2013, intact sediment cores were collected from
the mudflats of the fertilized and reference creeks at low tide (n=3 per creek
in June and October, n=6 per creek in August; 31 cm diameter x 15 cm deep).
These time periods reflected late spring, late summer, and early fall
conditions. Sediment cores were transported to Woods Hole Oceanographic
Institution\\u2019s mesocosm system (Woods Hole, MA). Cores were placed in
rectangular fiberglass tanks (2.7 m x 1.2 m x 0.8 m, l x w x d) that served as
a water bath to minimize extreme fluctuations in day \\u2013 night
temperatures. The mesocosm system is located outside, so cores experienced
ambient weather conditions.
Upon placement in the fiberglass tanks, the overlying water collected with
each sediment core was continuously recirculated (~9 cm deep). The cores
acclimated to the mesocosm system for 1 \\u2013 3 days, depending on weather,
as we applied the\\u00a013C label during sunny periods when BMA would be
productive. Visible epifauna (e.g., snails, shrimp) were removed to minimize
grazing on benthic microbes. At the beginning of each experiment, the
overlying water column was removed and replaced with filtered water from the
creek where the core was collected. We used 0.2 um filtered creek water to
minimize label uptake by water column microbes and recirculated the water
column to maintain well-mixed conditions. The isotopic label was added as
\\u00a013C-sodium bicarbonate (NaHCO3, 99 atom %, Sigma-Aldrich) to the water
column of each core in June and October and half of the cores from each creek
in August. The other half of the August cores received\\u00a013C-
labeled\\u00a0S. alterniflora\\u00a0detritus. This material was produced from a
separate experiment in which living\\u00a0S. alterniflora\\u00a0plants from PIE-
LTER were dosed with\\u00a013CO2\\u00a0for 3 h (Spivak & Reeve 2015).
Aboveground leaves were harvested after label exposure, dried (60 deg C), and
ground into a coarse powder that was evenly applied across the sediment
surface.\\u00a013C-S. alterniflora\\u00a0was only applied in August due to
availability of the labeled material. From here forward, experiments receiving
\\u00a013C-NaHCO3\\u00a0or\\u00a013C-S. alterniflora\\u00a0are referred to as BMA
or\\u00a0S. alterniflora\\u00a0experiments, respectively, to reflect the
autotrophic source of carbon to bacteria. On average (+/- standard error,
S.E.), the cores received 11.90 +/- 0.07 mg, 10.90 +/- 0.05, and 10.97 +/-
0.09 mg\\u00a013C from NaHCO3\\u00a0application in June, August, and October,
respectively, and 3.17 +/- 0.12 mg\\u00a013C from the\\u00a0S.
alterniflora\\u00a0detritus in August. The\\u00a013C label, as
NaHCO3\\u00a0or\\u00a0S. alterniflora, was applied for four hours between 11:00
\\u2013 15:00 h before the overlying water was removed and the cores were
rinsed with at least three volumes of filtered creek water to remove unused
label. The four hour sampling period was based on results from a preliminary
study demonstrating that this timeframe was sufficient for detecting the label
in algal and bacterial lipids. After the final rinse, the overlying water
column was replaced with filtered creek water and recirculated for the
duration of the experiments.\\u00a0
Sediment samples for organic matter composition were collected by placing a
hard plastic sleeve around a polyvinyl chloride (PVC) corer (5 cm diameter x
15 cm deep) and then removing the corer. The plastic sleeve remained in place
to maintain the integrity of the sediment column and mark the core location
(Spivak 2015). The top 0.5 cm of each core was collected into pre-combusted
vials and frozen (-80 deg C) until analysis for total organic carbon and
nitrogen content and stable isotopes (d13C, d15N) and lipid biomarker
composition. Adjacent samples for benthic chlorophyll were collected with
smaller cores (1.5 cm diameter x 1 cm deep) into glass vials and frozen (-20
deg C) until analysis. Additional sediment cores for organic matter
composition and benthic chlorophyll were collected 4, 8, 24, and 48 h after
the\\u00a013C-labeled NaHCO3\\u00a0was applied in June, August, and October and
4, 8, 24, and 144h after the\\u00a013C-labeled\\u00a0S. alterniflora\\u00a0was
applied in August.\\u00a0
Lipid biomarker compounds were extracted using a modified Bligh and Dyer
(1959) method. Sediment samples were extracted with a chloroform : methylene
chloride : phosphate buffer saline mixture (2:1:0.8, v:v:v) using a microwave-
accelerated reaction system (MARS6); samples were heated to 80 deg C for 10
min with continuous stirring. Following extraction, samples were partitioned
and the organic phase was removed. The total lipid extract was concentrated
under N2\\u00a0and samples were separated on silica gel columns by eluting with
chloroform, acetone (F1/2), and methanol (F3) (Guckert et al. 1985). The F3
(phospholipids) was dried under N2\\u00a0and saponified with 0.5 M NaOH at 70
deg C for 4 h. Saponified samples were acidified and extracted three times
with hexane. The extract was methylated with acidic methanol (95:5 methanol:
HCl) and heated overnight at 70 deg C to form fatty acid methyl esters (FAME).
Samples were analyzed with an Agilent 7890 gas chromatograph with an effluent
split ~70:30 between a 5975C mass spectrometer and a flame ionization
detector. Peaks were separated on an Agilent DB-5 ms column (60 m, 0.25 mm
inner diameter, 0.25 um film). FAME concentrations were quantified using
methyl heneicosanoate as an internal standard. FAs are designated A:BwC, 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 \\u2018w\\u2019 end of the
molecule. The prefixes \\u2018i\\u2019 and \\u2018a\\u2019 refer to iso and
anteiso methyl branched FAs and indicate whether the methyl group is attached
to the penultimate or antepenulttimate carbon atoms (Bianchi & Canuel 2011).";
String awards_0_award_nid "529582";
String awards_0_award_number "OCE-1233678";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1233678";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "David L. Garrison";
String awards_0_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Sediment PLFA Concentrations
Amanda Spivak, PI
Version 8 December 2016";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2016-12-10T00:55:15Z";
String date_modified "2019-04-05T17:05:52Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.669693.1";
String history
"2024-04-19T15:53:32Z (local files)
2024-04-19T15:53:32Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_669693.das";
String infoUrl "https://www.bco-dmo.org/dataset/669693";
String institution "BCO-DMO";
String instruments_0_acronym "Gas Chromatograph";
String instruments_0_dataset_instrument_description "Analyzed samples";
String instruments_0_dataset_instrument_nid "669738";
String instruments_0_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)";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB02/";
String instruments_0_instrument_name "Gas Chromatograph";
String instruments_0_instrument_nid "661";
String instruments_0_supplied_name "Agilent 7890 gas chromatograph";
String instruments_1_acronym "Mass Spec";
String instruments_1_dataset_instrument_description "Analyzed samples";
String instruments_1_dataset_instrument_nid "669737";
String instruments_1_description "General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB16/";
String instruments_1_instrument_name "Mass Spectrometer";
String instruments_1_instrument_nid "685";
String instruments_1_supplied_name "5975C mass spectrometer";
String instruments_2_dataset_instrument_description "Used to collect core samples";
String instruments_2_dataset_instrument_nid "669699";
String instruments_2_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/";
String instruments_2_instrument_name "Push Corer";
String instruments_2_instrument_nid "628287";
String instruments_2_supplied_name "Core";
String instruments_3_acronym "FID";
String instruments_3_dataset_instrument_description "Analyzed samples";
String instruments_3_dataset_instrument_nid "669739";
String instruments_3_description "A flame ionization detector (FID) is a scientific instrument that measures the concentration of organic species in a gas stream. It is frequently used as a detector in gas chromatography. Standalone FIDs can also be used in applications such as landfill gas monitoring, fugitive emissions monitoring and internal combustion engine emissions measurement in stationary or portable instruments.";
String instruments_3_instrument_name "Flame Ionization Detector";
String instruments_3_instrument_nid "644600";
String instruments_3_supplied_name "Flame ionization detector";
String keywords "4w6, 5w3, 6w3, a13, a15, a17, a19, bco, bco-dmo, biological, c12, c13, c14, c15, c16, c17, c18, c19, c20, c20_4w6, c20_5w3, c21, c22, c22_5, c22_6w3, c23, c24, c26, c28, chemical, data, dataset, dmo, erddap, estuary, experiment, i13, i14, i15, i16, i17, i19, management, me10, me10_16, month, oceanography, office, preliminary, timepoint, total, totalFA, unsat, unsatC22";
String license "https://www.bco-dmo.org/dataset/669693/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/669693";
String param_mapping "{'669693': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/669693/parameters";
String people_0_affiliation "Woods Hole Oceanographic Institution";
String people_0_affiliation_acronym "WHOI";
String people_0_person_name "Amanda Spivak";
String people_0_person_nid "529580";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI BCO-DMO";
String people_1_person_name "Hannah Ake";
String people_1_person_nid "650173";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "benthic_PP_at_TIDE";
String projects_0_acronym "benthic_PP_at_TIDE";
String projects_0_description
"Extracted from the NSF award abstract:
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?
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.";
String projects_0_end_date "2015-08";
String projects_0_geolocation "Plum Island Estuary, Rowley Massachusetts";
String projects_0_name "Eutrophication Effects on Sediment Metabolism and Benthic Algal-bacterial Coupling: An Application of Novel Techniques in a LTER Estuary";
String projects_0_project_nid "529583";
String projects_0_start_date "2012-09";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Raw concentrations of individual PLFA compounds from Massachusetts from 2012-2015.";
String title "Raw concentrations of individual PLFA compounds from Massachusetts from 2012-2015.";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.