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Dataset Title:  Experimental results: Remineralization experiments to assess the ability of
natural assemblages of bacteria to utilize DOM produced under Si and N
limitation (SBDOM project, SBC LTER project)
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_518508)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
 
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Things You Can Do With Your Graphs

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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  species {
    String bcodmo_name "species";
    String description "Name of the species.";
    String long_name "Species";
    String units "text";
  }
  treatment {
    String bcodmo_name "treatment";
    String description "Treatment condition.";
    String long_name "Treatment";
    String units "text";
  }
  replicate {
    Byte _FillValue 127;
    Byte actual_range 1, 2;
    String bcodmo_name "replicate";
    String description "Replicate number.";
    String long_name "Replicate";
    String units "integer";
  }
  time_point {
    Byte _FillValue 127;
    Byte actual_range 0, 20;
    String bcodmo_name "time_point";
    String description "Sampling time point.";
    String long_name "Time Point";
    String units "integer";
  }
  days_elapsed {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 112.0;
    String bcodmo_name "time_elapsed";
    String description "Number of days elapsed since the start of the experiment.";
    String long_name "Days Elapsed";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
    String units "number";
  }
  DOC {
    Float32 _FillValue NaN;
    Float32 actual_range 59.2, 110.4;
    String bcodmo_name "DOC";
    String description "Dissolved organic carbon.";
    String long_name "DOC";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
    String units "micromoles per Liter (umol/L)";
  }
  DOC_sd {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 6.1;
    String bcodmo_name "standard deviation";
    Float64 colorBarMaximum 50.0;
    Float64 colorBarMinimum 0.0;
    String description "Standard deviation of DOC.";
    String long_name "DOC Sd";
    String units "micromoles per Liter (umol/L)";
  }
  TDN {
    Float32 _FillValue NaN;
    Float32 actual_range 5.0, 23.9;
    String bcodmo_name "Total Dissolved Nitrogren";
    String description "Total dissolved nitrogen.";
    String long_name "TDN";
    String units "micromoles per Liter (umol/L)";
  }
  TDN_sd {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 1.4;
    String bcodmo_name "standard deviation";
    Float64 colorBarMaximum 50.0;
    Float64 colorBarMinimum 0.0;
    String description "Standard deviation of TDN.";
    String long_name "TDN SD";
    String units "micromoles per Liter (umol/L)";
  }
  NO3_NO2 {
    String bcodmo_name "NO3_NO2";
    String description "Nitrate and nitrite.";
    String long_name "NO3 NO2";
    String units "micromoles per Liter (umol/L)";
  }
  NH4 {
    String bcodmo_name "Ammonium";
    String description "Concentration of NH4.";
    String long_name "NH4";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AMONAAZX/";
    String units "micromoles per Liter (umol/L)";
  }
  PO4 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.16, 6.03;
    String bcodmo_name "PO4";
    String description "Concentration of PO4.";
    String long_name "Mass Concentration Of Phosphate In Sea Water";
    String units "micromoles per Liter (umol/L)";
  }
  dSi {
    Float32 _FillValue NaN;
    Float32 actual_range 0.07, 12.78;
    String bcodmo_name "unknown";
    String description "Dissolved SO4.";
    String long_name "D Si";
    String units "micromoles per Liter (umol/L)";
  }
  bact_abund_FCM {
    Float32 _FillValue NaN;
    Float32 actual_range 9.01e+7, 5.6700001e+9;
    String bcodmo_name "unknown";
    String description "Bacterial cell abundance measured via flow cytometer using SYBR Green stain.";
    String long_name "Bact Abund FCM";
    String units "cells per Liter (cells/L)";
  }
  bact_abund_DAPI {
    Float32 _FillValue NaN;
    Float32 actual_range 5.1e+8, 1.8e+9;
    String bcodmo_name "unknown";
    String description "Bacterial cell abundance measured via epifluorescence microscopy using DAPI stain.";
    String long_name "Bact Abund DAPI";
    String units "cells per Liter (cells/L)";
  }
  bact_abund_DAPI_sd {
    Float32 _FillValue NaN;
    Float32 actual_range 6.7e+7, 4.7e+8;
    String bcodmo_name "standard deviation";
    Float64 colorBarMaximum 50.0;
    Float64 colorBarMinimum 0.0;
    String description "Standard deviation of bact_abund_DAPI.";
    String long_name "Bact Abund DAPI Sd";
    String units "cells per Liter (cells/L)";
  }
  bact_prod {
    Float32 _FillValue NaN;
    Float32 actual_range 7.8, 2136.64;
    String bcodmo_name "unknown";
    String description "Bacterial production measured via 3H leucine uptake.";
    String long_name "Bact Prod";
    String units "picomoles Leucine per Liter per hour (pmol Leu/L/hr)";
  }
  bact_prod_sd {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 197.78;
    String bcodmo_name "standard deviation";
    Float64 colorBarMaximum 50.0;
    Float64 colorBarMinimum 0.0;
    String description "Standard deviation of bact_prod.";
    String long_name "Bact Prod Sd";
    String units "picomoles Leucine per Liter per hour (pmol Leu/L/hr)";
  }
  specifc_growth_rate {
    Float32 _FillValue NaN;
    Float32 actual_range 0.1, 1.9;
    String bcodmo_name "unknown";
    String description "Specific growth rate (µ) over exponential growth phase.";
    String long_name "Specifc Growth Rate";
    String units "per day";
  }
  bact_growth_eff {
    Byte _FillValue 127;
    Byte actual_range 8, 48;
    String bcodmo_name "unknown";
    String description "Bacterial growth efficiency over exponential growth phase.";
    String long_name "Bact Growth Eff";
    String units "unitless";
  }
  DNA_sampled {
    String bcodmo_name "unknown";
    String description "yes = sample was collected; analyzed samples still in QC.";
    String long_name "DNA Sampled";
    String units "yes or no";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"S. marinoi experimental design:  
 DOM was harvested from cultures of S. marinoi 48 hours after the indicated
nutrient became deplete. Harvested media was 2x filtered through 0.2 um
filters. Ambient seawater was the aged seawater media in which the
phytoplankton were grown. Media (6L) and inoculum (2L, 1.2-um filtered water
from the Santa Barbara Channel) were combined in a spigoted polycarbonate
carboy and incubated in the dark at 14C for 4 months.
 
C. socialis experimental design:  
 DOM was harvested from cultures of C. socialis 48 hours after the indicated
nutrient became deplete. Harvested media was 2x filtered through 0.2 um
filters. Ambient seawater was the aged seawater media in which the
phytoplankton were grown. Media (6L) and inoculum (2L, 1.2-um filtered water
from the Santa Barbara Channel) were combined in a spigoted polycarbonate
carboy and incubated in the dark at 14C for 4 months.
 
T. weissflogii experimental design:  
 DOM was harvested from cultures of T. weissflogii 48 hours after the
indicated nutrient became deplete. Harvested media was 2x filtered through 0.2
um filters. Ambient seawater was the aged seawater media in which the
phytoplankton were grown. Media (6L) and inoculum (2L, 1.2-um filtered water
from the Santa Barbara Channel) were combined in a spigoted polycarbonate
carboy and incubated in the dark at 14C for 4 months.
 
O. aurita experimental design:  
 DOM was harvested from cultures of O. aurita 48 hours after the indicated
nutrient became deplete. Harvested media was 2x filtered through 0.2 um
filters. Ambient seawater was the aged seawater media in which the
phytoplankton were grown. This experiment included full-volume inorganic
nutrient controls (ambient seawater with added nitrate and phosphate or
silicate and phosphate, at concentrations comparable to the Si-limited and
N-limited treatments, respectively) and small-volume (2L, same media:inoculum
ratio) controls to look at carry-over from the phytoplankton media that were
sampled less frequently and with fewer replicates (ambient seawater plus f/2
and ambient seawater plus filtered media from an O. aurita culture in
exponential growth, both at concentrations comparable to those at the start of
the O. aurita batch culture grow-ups). Media (6L) and inoculum (2L, 1.2-um
filtered water from the Santa Barbara Channel) were combined in a spigoted
polycarbonate carboy and incubated in the dark at 14C for 4 months.";
    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 
"Remineralization Experiments 
 Project: SBDOM 
 PI: Craig Carlson (UC Santa Barbara, MSI) 
 Co-PI: Mark Brzezinksi (UC Santa Barbara, MSI) 
 Version: 09 July 2014 
 Notes: BDL = Below Detection Limit (0.20 for NO3_NO2; 0.10 for NH4 and PO4) 
        Lack of standard deviation value indicates replicate was discarded for obvious 
          contamination and is not reflected in mean value.";
    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 "2014-07-09T18:53:14Z";
    String date_modified "2019-08-28T18:12:35Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.518508.1";
    String history 
"2022-08-13T00:58:00Z (local files)
2022-08-13T00:58:00Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_518508.das";
    String infoUrl "https://www.bco-dmo.org/dataset/518508";
    String institution "BCO-DMO";
    String keywords "abund, ammonium, bact, bact_abund_DAPI, bact_abund_DAPI_sd, bact_abund_FCM, bact_growth_eff, bact_prod, bact_prod_sd, bco, bco-dmo, biological, chemical, chemistry, commerce, concentration, dapi, data, dataset, days, days_elapsed, department, dmo, dna, DNA_sampled, doc, DOC_sd, dSi, earth, Earth Science > Oceans > Ocean Chemistry > Phosphate, eff, elapsed, erddap, fcm, growth, management, mass, mass_concentration_of_phosphate_in_sea_water, nh4, nitrate, nitrite, no2, no3, NO3_NO2, ocean, oceanography, oceans, office, phosphate, po4, point, preliminary, prod, rate, replicate, sampled, science, sea, seawater, species, specifc, specifc_growth_rate, tdn, TDN_sd, time, time_point, treatment, water";
    String keywords_vocabulary "GCMD Science Keywords";
    String license "https://www.bco-dmo.org/dataset/518508/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/518508";
    String param_mapping "{'518508': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/518508/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 "Lead 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 "Woods Hole Oceanographic Institution";
    String people_2_affiliation_acronym "WHOI BCO-DMO";
    String people_2_person_name "Shannon Rauch";
    String people_2_person_nid "51498";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "SBDOM,SBC LTER";
    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 projects_1_acronym "SBC LTER";
    String projects_1_description 
"From http://www.lternet.edu/sites/sbc
The Santa Barbara Coastal LTER is located in the coastal zone of southern California near Santa Barbara. It is bounded by the steep east-west trending Santa Ynez Mountains and coastal plain to the north and the unique Northern Channel Islands archipelago to the south. Santa Barbara Coastal Long-Term Ecological Research (SBC) Project is headquartered at the University of California, Santa Barbara, and is part of the National Science Foundation’s (NSF) Long-Term Ecological Research (LTER) Network.
The research focus of SBC LTER is on ecological systems at the land-ocean margin. Although there is increasing concern about the impacts of human activities on coastal watersheds and nearshore marine environments, there have been few long-term studies of the linkages among oceanic, reef, sandy beaches, wetland, and upland habitats. SBC LTER is helping to fill this gap by studying the effects of oceanic and coastal watershed influences on kelp forests in the Santa Barbara Channel located off the coast of southern California. The primary research objective of SBC LTER is to investigate the relative importance of land vs. ocean processes in structuring giant kelp (Macrocystis pyrifera) forest ecosystems for different conditions of land use, climate and ocean influences.
SBC LTER Data: The Santa Barbara Coastal (SBC) LTER data are managed by and available directly from the SBC project data site URL shown above.  If there are any datasets listed below, they are data sets that were collected at or near the SBC LTER sampling locations, and funded by NSF OCE as ancillary projects related to the SBC LTER core research themes. See the SBC LTER Data Overview page for access to data and information about data management policies.";
    String projects_1_geolocation "Southern California Coastal Zone";
    String projects_1_name "Santa Barbara Coastal Long Term Ecological Research site";
    String projects_1_project_nid "2227";
    String projects_1_project_website "http://sbc.lternet.edu/";
    String projects_1_start_date "2000-04";
    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 "Culture studies of diatoms that dominate spring blooms in the Santa Barbara Channel were used to examine the effects of N and Si stress on the magnitude of production and the chemical composition of DOM (see the BIB Experiments dataset). The ability of natural assemblages of bacteria to utilize DOM produced under Si and N limitation was then assessed using remineralization experiments. Species examined in the remineralization experiments include: Skeletonema marinoi, Chaetoceros socialis, Thalassiosira weissflogii, and Odontella aurita.";
    String title "Experimental results: Remineralization experiments to assess the ability of natural assemblages of bacteria to utilize DOM produced under Si and N limitation (SBDOM project, SBC LTER project)";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

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.


 
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