Accessing BCO-DMO data
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| Dataset Title: | [SBDOM11 mini-remineralization expt.] - Dilution batch-culture bioassay (remineralization) experiments from SBDOM11 project cruise from R/V Point Sur PS1103 in the Santa Barbara Channel, May 2011 (SBDOM project, SBC LTER project) (Mechanisms controlling the production and fate of DOM during diatom blooms) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_718117) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
Sample {
String bcodmo_name "sample";
String description "Internal experiment ID; A/B = replicate bottles";
String long_name "Sample";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
sta_id {
Float32 _FillValue NaN;
Float32 actual_range 7.0, 24.0;
String bcodmo_name "station";
String description "station where water for experiment was collected";
String long_name "Sta Id";
String units "unitless";
}
bottle {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 2, 11;
String bcodmo_name "bottle";
String description "rosette bottle from which water for experiment was drawn";
String long_name "Bottle";
String units "unitless";
}
Initiation_date {
String bcodmo_name "date_start";
String description "local date when experiment was begun";
String long_name "Initiation Date";
String source_name "Initiation_date";
String time_precision "1970-01-01";
String units "unitless";
}
Initiation_time {
String bcodmo_name "time_start";
String description "local time when experiment was begun";
String long_name "Initiation Time";
String units "unitless";
}
Timepoint {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 0, 8;
String bcodmo_name "time_point";
String description "sampling timepoint; from 0 (post-initiation) through 8";
String long_name "Timepoint";
String units "unitless";
}
Date {
String bcodmo_name "date_local";
String description "local date on which timepoint was sampled";
String long_name "Date";
String time_precision "1970-01-01";
String units "unitless";
}
DOC_sampling_time {
String bcodmo_name "time_local";
String description "local time at which DOC was sampled";
String long_name "DOC Sampling Time";
String units "unitless";
}
DOC_Bottle_A {
Float32 _FillValue NaN;
Float32 actual_range 50.5, 73.1;
String bcodmo_name "DOC";
String description "DOC concentration in Bottle A at specified timepoint (nd missing data = failed QC)";
String long_name "DOC Bottle A";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
String units "micromol/liter";
}
DOC_A_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.1, 2.4;
String bcodmo_name "DOC";
String description "standard deviation between injections on Shimadzu instrument while measuring DOC in Bottle A at specified timepoint";
String long_name "DOC A St Dev";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
String units "micromol/liter";
}
DOC_Bottle_B {
Float32 _FillValue NaN;
Float32 actual_range 50.5, 71.6;
String bcodmo_name "DOC";
String description "DOC concentration in Bottle B at specified timepoint (nd missing data = failed QC)";
String long_name "DOC Bottle B";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
String units "micromol/liter";
}
DOC_B_st_dev {
Float32 _FillValue NaN;
Float32 actual_range 0.1, 2.8;
String bcodmo_name "DOC";
String description "standard deviation between injections on Shimadzu instrument while measuring DOC in Bottle B at specified timepoint";
String long_name "DOC B St Dev";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
String units "micromol/liter";
}
Bact_abun_sampling_time {
String bcodmo_name "cell_concentration";
String description "local time at which bacterial abundance was sampled";
String long_name "Bact Abun Sampling Time";
String units "unitless";
}
Bact_abun_A {
Float32 _FillValue NaN;
Float32 actual_range 6.56e+7, 2.18e+9;
String bcodmo_name "cell_concentration";
String description "Bacterial abundance in Bottle A at specified timepoint";
String long_name "Bact Abun A";
String units "cells/liter";
}
Bact_abun_B {
Float32 _FillValue NaN;
Float32 actual_range 6.52e+7, 2.1e+9;
String bcodmo_name "cell_concentration";
String description "Bacterial abundance in Bottle B at specified timepoint";
String long_name "Bact Abun B";
String units "cells/liter";
}
DNA_sampling_time {
String bcodmo_name "time_local";
String description "local time at which DNA was sampled";
String long_name "DNA Sampling Time";
String units "unitless";
}
Pyrosequencing_barcode {
String bcodmo_name "sequence";
String description "multiplexing barcode corresponding to this sample; in the combined dataset available under SRA accession number SRR1222603";
String long_name "Pyrosequencing Barcode";
String units "unitless";
}
mu_growth_A {
Float32 _FillValue NaN;
Float32 actual_range 0.18, 1.17;
String bcodmo_name "growth";
String description "specific growth rate of bacterial cells in Bottle A; calculated over the exponential growth phase of the experiment";
String long_name "Mu Growth A";
String units "cells/day";
}
mu_growth_B {
Float32 _FillValue NaN;
Float32 actual_range 0.23, 1.02;
String bcodmo_name "growth";
String description "specific growth rate of bacterial cells in Bottle B; calculated over the exponential growth phase of the experiment";
String long_name "Mu Growth B";
String units "cells/day";
}
BGE_A {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 16, 70;
String bcodmo_name "growth";
String description "bacterial growth efficiency (percent) in Bottle A; calculated over the exponential growth phase";
String long_name "BGE A";
String units "unitless";
}
BGE_B {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 16, 75;
String bcodmo_name "growth";
String description "bacterial growth efficiency (percent) in Bottle B; calculated over the exponential growth phase";
String long_name "BGE B";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Dilution batch-culture bioassay experiments were established 11 May 2011 - 15
May 2011 on the SBDOM 11 cruise using water samples collected from the upper
8m of the water column. Water was gravity-filtered from the sampling Niskin
bottle through two mixed cellulose ester filters (1.2 \\u00b5m and 0.2
\\u00b5m). Duplicate 500 mL polycarbonate bottles were filled with 375 mL 0.2
\\u00b5m filtrate (filter sterilized media) and 125 mL 1.2 \\u00b5m filtrate
(bacterial inoculum) collected from the same cast. Bottles were incubated in
the dark at 11degrees C for 10 weeks. Samples for bacterial abundance, DOM,
and community composition by DNA were collected by decanting from the bottle
at specified intervals.
DOC was quantified by high-temperature combustion on a modified Shimadzu
TOC-V. We used 1.5 \\u00b5M DOC as a detection limit for these experiments.
Bacterial abundance was measured using a BD LSRII flow cytometer with an
autosampler attachment. Samples were preserved in sterile cryovials with 0.2%
final concentration paraformaldehyde, then stored frozen until analysis.
Samples were stained with SYBR Green I for enumeration.
DNA was collected from duplicate bottles combined (to conserve volume); 125 mL
from each bottle was vacuum-filtered onto a 0.2 \\u00b5m polyethersulfone
filter and frozen. Samples were lysed in sucrose lysis buffer with 1% w/v
sodium dodecyl sulfate and 0.2 mg mL-1 proteinase-K, and genomic DNA was
extracted using a Qiagen DNEasy silica centrifugation kit. DNA was used to
conduct multiplex amplicon pyrosequencing using primers 8F and 338R, following
the protocol of Nelson et al. (2014; doi: 10.1111/1462-2920.12241). Sequence
analysis was conducted in mothur (Schloss et al. 2009; doi:
10.1128/AEM.01541-09) using a non-redundant subset of the SILVA SSU Ref 16S
alignment database (v111) curated as in Nelson et al. (2014).";
String awards_0_award_nid "54995";
String awards_0_award_number "OCE-0850857";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0850857";
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
"cruise SBDOM11 mini-remineralizations
C. Carlson, M. Brzezinski (UCSB)
version: 2017-10-30";
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 "2017-10-30T20:49:42Z";
String date_modified "2019-08-28T17:37:08Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.718117.1";
String history
"2024-11-23T07:54:35Z (local files)
2024-11-23T07:54:35Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_718117.html";
String infoUrl "https://www.bco-dmo.org/dataset/718117";
String institution "BCO-DMO";
String instruments_0_acronym "Shimadzu TOC-V";
String instruments_0_dataset_instrument_description "Used to measure dissolved organic carbon concentrations";
String instruments_0_dataset_instrument_nid "718508";
String instruments_0_description "A Shimadzu TOC-V Analyzer measures DOC by high temperature combustion method.";
String instruments_0_instrument_external_identifier "http://onto.nerc.ac.uk/CAST/124";
String instruments_0_instrument_name "Shimadzu TOC-V Analyzer";
String instruments_0_instrument_nid "603";
String instruments_0_supplied_name "modified Shimadzu TOC-V";
String instruments_1_acronym "Automated Sequencer";
String instruments_1_dataset_instrument_description "used to conduct multiplex amplicon pyrosequencing";
String instruments_1_dataset_instrument_nid "718511";
String instruments_1_description "General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.";
String instruments_1_instrument_name "Automated DNA Sequencer";
String instruments_1_instrument_nid "649";
String instruments_2_acronym "Flow Cytometer";
String instruments_2_dataset_instrument_description "BD LSRII flow cytometer with an autosampler attachment used to obtain bacterial abundance.";
String instruments_2_dataset_instrument_nid "718509";
String instruments_2_description
"Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB37/";
String instruments_2_instrument_name "Flow Cytometer";
String instruments_2_instrument_nid "660";
String instruments_2_supplied_name "BD LSRII flow cytometer";
String instruments_3_acronym "Thermal Cycler";
String instruments_3_dataset_instrument_description "used to conduct multiplex amplicon pyrosequencing";
String instruments_3_dataset_instrument_nid "718510";
String instruments_3_description
"General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)";
String instruments_3_instrument_name "PCR Thermal Cycler";
String instruments_3_instrument_nid "471582";
String keywords "abun, bact, Bact_abun_A, Bact_abun_B, Bact_abun_sampling_time, barcode, bco, bco-dmo, bge, BGE_A, BGE_B, biological, bottle, chemical, commerce, data, dataset, date, department, dev, dmo, dna, DNA_sampling_time, doc, DOC_A_st_dev, DOC_B_st_dev, DOC_Bottle_A, DOC_Bottle_B, DOC_sampling_time, erddap, growth, initiation, Initiation_time, management, mu_growth_A, mu_growth_B, oceanography, office, preliminary, pyrosequencing, Pyrosequencing_barcode, sample, sampling, sta, sta_id, time, timepoint";
String license "https://www.bco-dmo.org/dataset/718117/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/718117";
String param_mapping "{'718117': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/718117/parameters";
String people_0_affiliation "University of California-Santa Barbara";
String people_0_affiliation_acronym "UCSB-MSI";
String people_0_person_name "Craig Carlson";
String people_0_person_nid "50575";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of California-Santa Barbara";
String people_1_affiliation_acronym "UCSB-MSI";
String people_1_person_name "Mark A. Brzezinski";
String people_1_person_nid "50663";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "University of California-Santa Barbara";
String people_2_affiliation_acronym "UCSB-MSI";
String people_2_person_name "Emma Wear";
String people_2_person_nid "51542";
String people_2_role "Student";
String people_2_role_type "related";
String people_3_affiliation "University of California-Santa Barbara";
String people_3_affiliation_acronym "UCSB-MSI";
String people_3_person_name "Maverick Carey";
String people_3_person_nid "720215";
String people_3_role "Technician";
String people_3_role_type "related";
String people_4_affiliation "University of California-Santa Barbara";
String people_4_affiliation_acronym "UCSB-MSI";
String people_4_person_name "Elisa Halewood";
String people_4_person_nid "51543";
String people_4_role "Technician";
String people_4_role_type "related";
String people_5_affiliation "University of California-Santa Barbara";
String people_5_affiliation_acronym "UCSB-MSI";
String people_5_person_name "Ms Anna James";
String people_5_person_nid "471722";
String people_5_role "Technician";
String people_5_role_type "related";
String people_6_affiliation "Woods Hole Oceanographic Institution";
String people_6_affiliation_acronym "WHOI BCO-DMO";
String people_6_person_name "Nancy Copley";
String people_6_person_nid "50396";
String people_6_role "BCO-DMO Data Manager";
String people_6_role_type "related";
String project "SBDOM";
String projects_0_acronym "SBDOM";
String projects_0_description
"This project is also affiliated with the Plumes and Blooms project.
Data:
The following data files have been submitted to BCO-DMO but are not yet available online. Data are restricted until June 2016. Please contact the PI for access prior to public availability:
-- SBDOM10 and SBDOM11 CTD and Niskin bottle data.
The following are available online (see 'Datasets' heading below):
-- SBDOM10 and SBDOM11 cruise plans (available online on deployment pages: PS1009, PS1103)
-- SBDOM10 and SBDOM11 event logs (available online; see 'Datasets' below)
-- Laboratory-based Bloom in a Bottle (BIB) Experiment
-- Laboratory-based Remineralization Experiments
-- SBDOM10 and SBDOM11 data summaries (including CTD data, nutrients, and bacterial production)
Project Description from NSF Award Proposal and Abstract:
Diatom blooms are known to produce prodigious quantities of DOM upon entering nutrient stress with a chemical composition that varies with the type of nutrient limitation (Si or N). This variable composition likely influences the nutritional value of DOM to microbes driving species successions towards functional groups of heterotrophic prokaryotes that are best able to metabolize particular forms of DOM. To date each side of this coupled system of production/consumption has been examined independently. A few studies have examined how limitation by different limiting nutrients affects the chemical character of the DOM produced by phytoplankton, while others have focused on the fate of DOM without detailed understanding of the mechanisms influencing its initial chemical composition.
We propose to investigate the mechanisms determining the character and fate of DOM produced during temperate diatom blooms. Specifically we will investigate how physiological stress on diatoms induced by different limiting nutrients influences the production, chemical composition of DOM and the microbial community structure that respond to it to better understand the mechanisms driving the accumulation and persistence of DOM in marine systems. The research will involve both laboratory and field experiments. The novel aspects of this work are:
1) We will investigate how limitation by either N or Si impacts the quantity and chemical composition of the DOM released by diatoms.
2) Assess how the differences in the chemical composition of the DOM produced under N or Si limitation affect its lability by examining the productivity, growth efficiency and community structure of heterotrophic bacterioplankton responding to the release of substrates.
3) Predicted DOM dynamics based on (1) and (2) will be tested in the field during diatom blooms in the Santa Barbara Channel, California.
While experiments investigating aspects of either 1 or 2 have been conducted successfully in the past (Lancelot, 1983; Billen and Fontigny, 1987; Goldman et al., 1992; Carlson et al.,1999; Cherrier and Bauer, 2004; Conan et al., 2007) ours will be the first study to combine these approaches in an integrated assessment of the mechanisms governing both the production and fate of DOM produced by diatom blooms experiencing limitation by different nutrients.
References:
Lancelot, C. (1983). Factors affecting phytoplankton extracellular release in the Southern Bight of the North Sea. Marine Ecology Progress Series 12: 115-121.
Billen, G. and A. Fontigny (1987). Dynamics of a Phaeocystis -dominated spring bloom in Belgian coastal waters. II. Bacterioplankton dynamics. Mar. Ecol. Prog. Ser. 37: 249-257.
Goldman, J.C., D.A. Hansell and M.R. Dennett (1992). Chemical characterization of three large oceanic diatoms: potential impact on water column chemistry. Marine Ecology Progress Series 88: 257-270.
Carlson, C.A., N.R. Bates, H.W. Ducklow and D.A. Hansell (1999). Estimation of bacterial respiration and growth efficiency in the Ross Sea, Antarctica. Aquatic Microbial Ecology 19: 229-244.
Cherrier, J. and J.E. Bauer (2004). Bacterial utilization of transient plankton-derived dissolved organic carbon and nitrogen inputs in surface ocean waters. Aquatic Microbial Ecology 35(3): 229-241.
Conan, P., M. Sondegaard, T. Kragh, F. Thingstad, M. Pujo-Pay, P.J.l.B. Williams, S. Markager, G. Cauwet, N.H. Borch, D. Evans and B. Rieman (2007). Partitioning of organic production in marine plankton communities: The effects of inorganic nutrient ratios and community composition on new dissolved organic matter. Limnology and Oceanography 52(2): 753-765.";
String projects_0_end_date "2014-03";
String projects_0_geolocation "Pacific California, Santa Barbara Channel";
String projects_0_name "Mechanisms controlling the production and fate of DOM during diatom blooms";
String projects_0_project_nid "2226";
String projects_0_start_date "2009-04";
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 "This dataset includes results from dilution batch-culture bioassay experiments reporting bacterial abundance, growth rates, barcode sequences and DOC were from the SBDOM 11 cruise in May 2011.";
String title "[SBDOM11 mini-remineralization expt.] - Dilution batch-culture bioassay (remineralization) experiments from SBDOM11 project cruise from R/V Point Sur PS1103 in the Santa Barbara Channel, May 2011 (SBDOM project, SBC LTER project) (Mechanisms controlling the production and fate of DOM during diatom blooms)";
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.