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Dataset Title:  Bacterioplankton data from coral and coral mucus aquaria experiments conducted
at Bermuda Institute of Ocean Sciences in 2013
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_652849)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files | Make a graph
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
 
   Maximum ?
 
 treatment (unitless) ?              
 treatment_description (unitless) ?              
 tank (unitless) ?          1    9
 mesocosm (unitless) ?              
 timepoint_name (days) ?              
 timepoint_days (days) ?          0.0    11.99
 temp (Temperature, celsius) ?          24.5    26.9
 salinity (ppt) ?          36.32    38.6
 DAPI_count (cells per milliliter) ?          359000.0    2030000.0
 accession_number (unitless) ?              
 nonPigmentPico (cells per milliliter) ?          204000.0    7020000.0
 synechococcus (cells per milliliter) ?          39    108386
 picoeukaryote (cells per milliliter) ?          473    9883
 lowHeterotrophicBac (cells per milliliter) ?          8320.0    1780000.0
 highHeterotrophicBac (cells per milliliter) ?          196000.0    6550000.0
 SAR11 (cells per milliliter) ?          8310.0    515000.0
 rhodobacteracea (cells per milliliter) ?          8670.0    324000.0
 alteromonas (cells per milliliter) ?          0.0    98300.0
 vibrio (cells per milliliter) ?          0.0    55400.0
 thaumarchaeota (cells per milliliter) ?          0.0    80500.0
 euryarchaeota (cells per milliliter) ?          0.0    149000.0
 P04 (micromoles) ?          0.03    0.2
 N03_N02 (micromoles) ?          0.52    10.22
 Si04 (micromoles) ?          1.1    5.4
 N02 (micromoles) ?          0.06    0.48
 NH4 (micromoles) ?          0.3    7.09
 DOC (micromoles) ?          71.82    110.86
 bacGrowth_constant_mean (days -1) ?          -0.31    0.5
 bacGrazing_coefficient_mean (days -1) ?          -0.32    0.56
 synechococcusGrowth_constant_mean (days -1) ?          -1.18    0.03
 synechococcusGrazing_coefficient (days -1) ?          -1.21    -0.55
 SAR11Growth_constant_mean (days -1) ?          -0.91    1.19
 SAR11Grazing_coefficient (days -1) ?          -0.98    -0.26
 rhodobacteraceaGrowth_constant_mean (days -1) ?          -0.89    1.34
 rhodobacteraceaGrazing_coefficient (days -1) ?          -0.92    0.06
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  treatment {
    String description "mesocosm treatment; control; mucus addition; and coral with artifical lights";
    String ioos_category "Unknown";
    String long_name "Treatment";
    String units "unitless";
  }
  treatment_description {
    String description "mesocosm condition; coral: presence or absence of colonies; mucus addition; or control";
    String ioos_category "Unknown";
    String long_name "Treatment Description";
    String units "unitless";
  }
  tank {
    Byte _FillValue 127;
    Byte actual_range 1, 9;
    String description "tank number";
    String ioos_category "Unknown";
    String long_name "Tank";
    String units "unitless";
  }
  mesocosm {
    String description "treatment and tank number";
    String ioos_category "Unknown";
    String long_name "Mesocosm";
    String units "unitless";
  }
  timepoint_name {
    String description "day during duration of 12 day experiment";
    String ioos_category "Time";
    String long_name "Timepoint Name";
    String units "days";
  }
  timepoint_days {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 11.99;
    String description "timepoint within 12 day experiment";
    String ioos_category "Time";
    String long_name "Timepoint Days";
    String units "days";
  }
  temp {
    Float32 _FillValue NaN;
    Float32 actual_range 24.5, 26.9;
    String description "temperature in mesocosm at each timepoint";
    String ioos_category "Temperature";
    String long_name "Temperature";
    String units "celsius";
  }
  salinity {
    Float32 _FillValue NaN;
    Float32 actual_range 36.32, 38.6;
    Float64 colorBarMaximum 37.0;
    Float64 colorBarMinimum 32.0;
    String description "salinity in mesocosm at each timepoint";
    String ioos_category "Salinity";
    String long_name "Sea Water Practical Salinity";
    String units "ppt";
  }
  DAPI_count {
    Float32 _FillValue NaN;
    Float32 actual_range 359000.0, 2030000.0;
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "0 6-diamidino-2-phenyl dihydrochloride (DAPI) counts of picoplankton";
    String ioos_category "Statistics";
    String long_name "DAPI Count";
    String units "cells per milliliter";
  }
  accession_number {
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "SSU rRNA gene V4 region sequences; NCBI SRA Accession";
    String ioos_category "Statistics";
    String long_name "Accession Number";
    String units "unitless";
  }
  nonPigmentPico {
    Float32 _FillValue NaN;
    Float32 actual_range 204000.0, 7020000.0;
    String description "Non-pigmented picoplankton cells counted by flow cytometry";
    String ioos_category "Unknown";
    String long_name "Non Pigment Pico";
    String units "cells per milliliter";
  }
  synechococcus {
    Int32 _FillValue 2147483647;
    Int32 actual_range 39, 108386;
    String description "Synechococcus cells counted by flow cytometry";
    String ioos_category "Unknown";
    String long_name "Synechococcus";
    String units "cells per milliliter";
  }
  picoeukaryote {
    Int16 _FillValue 32767;
    Int16 actual_range 473, 9883;
    String description "picoeukaryote cells counted by flow cytometry";
    String ioos_category "Unknown";
    String long_name "Picoeukaryote";
    String units "cells per milliliter";
  }
  lowHeterotrophicBac {
    Float32 _FillValue NaN;
    Float32 actual_range 8320.0, 1780000.0;
    String description "Low DNA heterotropic bacteria counted by flow cytometry";
    String ioos_category "Unknown";
    String long_name "Low Heterotrophic Bac";
    String units "cells per milliliter";
  }
  highHeterotrophicBac {
    Float32 _FillValue NaN;
    Float32 actual_range 196000.0, 6550000.0;
    String description "High DNA concent heterotrophic bacteria counted by flow cytometry";
    String ioos_category "Unknown";
    String long_name "High Heterotrophic Bac";
    String units "cells per milliliter";
  }
  SAR11 {
    Float32 _FillValue NaN;
    Float32 actual_range 8310.0, 515000.0;
    String description "SAR11 cell counts by fluorescence in situ hybridization (FISH)";
    String ioos_category "Unknown";
    String long_name "SAR11";
    String units "cells per milliliter";
  }
  rhodobacteracea {
    Float32 _FillValue NaN;
    Float32 actual_range 8670.0, 324000.0;
    String description "Rhodobacteracea cell counts by fluorescence in situ hybridization (FISH)";
    String ioos_category "Unknown";
    String long_name "Rhodobacteracea";
    String units "cells per milliliter";
  }
  alteromonas {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 98300.0;
    String description "Alteromonas cell counts by fluorescence in situ hybridization (FISH)";
    String ioos_category "Unknown";
    String long_name "Alteromonas";
    String units "cells per milliliter";
  }
  vibrio {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 55400.0;
    String description "Vibrio cell counts by fluorescence in situ hybridization (FISH)";
    String ioos_category "Unknown";
    String long_name "Vibrio";
    String units "cells per milliliter";
  }
  thaumarchaeota {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 80500.0;
    String description "Thaumarchaeota cell counts by fluorescence in situ hybridization (FISH)";
    String ioos_category "Unknown";
    String long_name "Thaumarchaeota";
    String units "cells per milliliter";
  }
  euryarchaeota {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 149000.0;
    String description "Euryarchaeota cell counts by fluorescence in situ hybridization (FISH)";
    String ioos_category "Unknown";
    String long_name "Euryarchaeota";
    String units "cells per milliliter";
  }
  P04 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.03, 0.2;
    String description "phosphate in seawater samples";
    String ioos_category "Unknown";
    String long_name "P04";
    String units "micromoles";
  }
  N03_N02 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.52, 10.22;
    String description "nitrate + nitrate in seawater samples";
    String ioos_category "Unknown";
    String long_name "N03 N02";
    String units "micromoles";
  }
  Si04 {
    Float32 _FillValue NaN;
    Float32 actual_range 1.1, 5.4;
    String description "silicate in seawater samples";
    String ioos_category "Unknown";
    String long_name "Si04";
    String units "micromoles";
  }
  N02 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.06, 0.48;
    String description "nitrite in seawater samples";
    String ioos_category "Unknown";
    String long_name "N02";
    String units "micromoles";
  }
  NH4 {
    Float32 _FillValue NaN;
    Float32 actual_range 0.3, 7.09;
    Float64 colorBarMaximum 5.0;
    Float64 colorBarMinimum 0.0;
    String description "ammonium in seawater samples";
    String ioos_category "Dissolved Nutrients";
    String long_name "Mole Concentration Of Ammonium In Sea Water";
    String units "micromoles";
  }
  DOC {
    Float32 _FillValue NaN;
    Float32 actual_range 71.82, 110.86;
    String description "dissolved organic carbon in seawater samples";
    String ioos_category "Unknown";
    String long_name "DOC";
    String units "micromoles";
  }
  bacGrowth_constant_mean {
    Float32 _FillValue NaN;
    Float32 actual_range -0.31, 0.5;
    String description "k; mean bacterial growth constant";
    String ioos_category "Statistics";
    String long_name "Bac Growth Constant Mean";
    String units "days -1";
  }
  bacGrazing_coefficient_mean {
    Float32 _FillValue NaN;
    Float32 actual_range -0.32, 0.56;
    String description "g; mean bact grazing coefficient";
    String ioos_category "Statistics";
    String long_name "Bac Grazing Coefficient Mean";
    String units "days -1";
  }
  synechococcusGrowth_constant_mean {
    Float32 _FillValue NaN;
    Float32 actual_range -1.18, 0.03;
    String description "k; mean synechococcus growth constant";
    String ioos_category "Statistics";
    String long_name "Synechococcus Growth Constant Mean";
    String units "days -1";
  }
  synechococcusGrazing_coefficient {
    Float32 _FillValue NaN;
    Float32 actual_range -1.21, -0.55;
    String description "synechococcus grazing coefficient";
    String ioos_category "Unknown";
    String long_name "Synechococcus Grazing Coefficient";
    String units "days -1";
  }
  SAR11Growth_constant_mean {
    Float32 _FillValue NaN;
    Float32 actual_range -0.91, 1.19;
    String description "k; mean SAR11 growth constant";
    String ioos_category "Statistics";
    String long_name "SAR11 Growth Constant Mean";
    String units "days -1";
  }
  SAR11Grazing_coefficient {
    Float32 _FillValue NaN;
    Float32 actual_range -0.98, -0.26;
    String description "SAR11 grazing coefficient";
    String ioos_category "Unknown";
    String long_name "SAR11 Grazing Coefficient";
    String units "days -1";
  }
  rhodobacteraceaGrowth_constant_mean {
    Float32 _FillValue NaN;
    Float32 actual_range -0.89, 1.34;
    String description "k; mean Rhodobacteracea growth constant";
    String ioos_category "Statistics";
    String long_name "Rhodobacteracea Growth Constant Mean";
    String units "days -1";
  }
  rhodobacteraceaGrazing_coefficient {
    Float32 _FillValue NaN;
    Float32 actual_range -0.92, 0.06;
    String description "Rhodobacteracea grazing coefficient";
    String ioos_category "Unknown";
    String long_name "Rhodobacteracea Grazing Coefficient";
    String units "days -1";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Colonies of Porites astreoides corals (5-20 cm diameter, 30-90 g wet weight)
were removed from 3-9 m depth on the Bermudian reefs Hog Breaker (N 32
27.5\\u2019 W 64 49.8\\u2019), an unnamed reef (N 32 26.042\\u2019 W 64
49.248\\u2019), and Three Hills Shoal (N 32 41\\u2019 W 64 73.3\\u2019) in July
2013. Ten colonies were taken from each site in compliance with the Bermuda
Institute of Ocean Sciences (BIOS) Collection and Experimental Ethics Policy
and were considered Limited Impact Research and as such a collection permit
was not required. The colonies were immediately placed in collection bags at
depth, sealed and transported in a large collection cooler (greater than 1 h)
to the laboratory.\\u00a0 At BIOS, the colonies were allowed to acclimate to a
mesocosm housing and held in aerated, outdoor fiberglass mesocosms with a
flow-through seawater system fed with reef water for two (Three Hills Shoal
Reef colonies) or 15 days (all other colonies) prior to the start of the
experimental period.\\u00a0
 
For the experiment, the mesocosms consisted of nine, 30 L static aquaria that
were set up as previously described (de Putron et al. 2010). Inshore water
from 20 meters off shore and one meter in depth was used to fill the aquaria
and was pumped through a BIOS flow-through sample system that consisted of a
coarse mesh filter and holding tanks followed by a step filtration system of
50 um, then 5 um, to remove larger organisms including some planktonic
grazers. Mesocosms were then left static for the 12-day experiment. Mesocosms
were randomly arranged to consist of three control, three mucus addition, and
three coral mesocosms, with artificial lights providing 61 mol quanta m-2 s-1
photosynthetically active radiation during sunlight hours consistent with the
low end of known compensation ranges (3-233 mol quanta m-2 s-1 according to
Mass and colleagues (2007) to minimize bleaching. Mesocosms were covered with
a transparent plastic film cover and aerated with an air wand bubbler (de
Putron et al. 2010). Water was collected from the mesocosms via a syringe-
siphon system using silicon tubing.\\u00a0 Inline, combusted GF/F filters
(Whatman, Maidstone, UK) were attached for samples intended for dissolved
organic carbon (DOC) analysis. The reef water temperature, salinity, and
conductivity in all mesocosms was monitored daily throughout the experiment
using a YSI Professional Plus probe (Yellow Springs, Ohio).\\u00a0
 
Over the course of 12 days, the mesocosms were subjected to one of three
conditions: coral (presence/absence of colonies), mucus additions or control
(no additions).\\u00a0 For the coral mesocosms, the experimental corals (four
colonies per mesocosm, three mesocosms) were placed within the mesocosms on
days 0 through 4 and removed after water sampling on day 4. Corals were
removed for 48-hour until after the sampling procedure on day 6, where they
were held in running seawater similarly filtered as in the mesocosms, and
reintroduced back into their respective mesocosms from days 6 to 10 and
removed again after the sampling procedure on day 10. P. astreoides colonies
were not fed over the course of the 12-day experimental period. For the mucus
addition mesocosms, mucus was extracted from P. astreoides colonies (n = 18)
that were not utilized in the experiment and were maintained in a separate,
flow-through seawater tank.\\u00a0 These corals (n=18) were taken into the lab
and inverted on a funnel to collect mucus for 2 h, a timeframe determined from
a preliminary experiment, and the corals returned to the holding aquaria with
flow through seawater. Mucus from the additional colonies was pooled and 5 ml
was added to each mucus addition mesocosm on days 0.2, 2, 6 and 8.\\u00a0 Mucus
from the experimental corals (n = 12; named corals A-L from coral tanks 4, 5
and 6) was sampled for community composition prior to day 0, as well as at the
end of day 4 and at the end of day 10 of the experiment.\\u00a0 For the latter
two timepoints, the corals were removed from the experimental mesocosms for 48
hours.\\u00a0
 
Seawater samples (50 ml) for cell counts and fluorescence in situ
hybridization (FISH) analyses were taken daily from all mesocosms, fixed with
formalin to a final concentration of 10% in the dark for 20 min, and stored at
-80C.\\u00a0 Samples were thawed and 3-5 ml were filtered onto Irgalan Black
stained 25 mm, 0.2 um polycarbonate filters (Nucleopore, Whatman) under gentle
vacuum (100 mmHg) and stained with 1 ml of 0, 6-diamidino-2-phenyl
dihydrochloride (5 ug ml-1, DAPI, SIGMA-Aldrich, St. Louis, MO) (Porter and
Feig 1980). The filters were mounted onto slides with Resolve immersion oil
(high viscosity) (Resolve, Richard-Allan Scientific, Kalamazoo, MI) and stored
at \\u201320 degrees celsius. Slides were then enumerated using an AX70
epifluorescent microscope (Olympus, Tokyo, Japan) under ultraviolet excitation
at 100x magnification. At least 500 cells (10 fields) were counted for
picoplankton abundance.\\u00a0\\u00a0 \\u00a0
 
FISH was utilized to quantify the abundance of the major picoplankton
phylotypes present in the seawater and mucus, and was conducted using
previously published protocols and Cy3 labeled probes (Parsons et al. 2014).
The bacterial and archaeal groups quantified included the SAR11 clade (152R,
441R, 542R, 732R probes), Alteromonas spp. (AC137R), Vibrio spp. (127R),
Rhodobacteracea (536R), Euryarchaeota (Eury806) and Thaumarchaeota (Cren537).
Fixed seawater samples (3\\u20135 ml) were filtered onto 25 mm, 0.2 um
polycarbonate filters and stored at \\u221220 degrees celcius with desiccant.
Quarter filters were washed in 95% ethanol and then probed according to
previous protocols (Morris et al. 2002; Parsons et al. 2011, 2014). The cell
abundances of the picoplankton phylotypes mentioned above were then determined
using image analysis (Parsons et al. 2011, 2014). Detection of Cy3-positive
cells and their ratio to DAPI-positive cells was aided by image analysis using
an Olympus AX70 microscope (Olympus, Japan) equipped with a Toshiba 3CCD video
camera (IK-TU40A Toshiba, Japan), a computer assisted frame grabber and
appropriate dichroic filters (Morris et al. 2002; Carlson et al. 2010). Brief
exposure times of 1 and 5 seconds were used for DAPI and Cy3 image channels,
respectively.\\u00a0 Cy3 images were segmented with Image Pro Plus software
(Media Cybernetics, Bethesda, MD) and overlaid onto corresponding segmented
DAPI images (Parsons et al. 2014). Objects with overlapping signals in both
Cy3 and DAPI images were counted as probe positive. The negative control was
determined similarly and subtracted from the positive probe counts to correct
for autofluorescence and non-specific binding.\\u00a0 (For Grazing Rates
Processing, see below)
 
Seawater picoplankton biomass for nucleic acids was taken from all
experimental mesocosms on days 0, 2, 4, 6, 8, 10 and 12 of the experiment, and
from coral mucus extracted from the experimental corals on days 2, 4, and 10
and processing followed a method modified from Giovannoni and colleagues
(1990, 1996). 500 ml of water or 1 ml of coral mucus was filtered through a 47
mm, 0.2 um pore filter under gentle vacuum (100 mm Hg), placed into a 4 ml
cryovial and stored in 1 ml of sterile sucrose lysis buffer (20 mM EDTA, 400
mM NaCl, 0.75 M sucrose, 50 mM Tris.HCl) at -80 degrees celsius. For DNA
extractions of the tissue, mucus and coral samples, sodium dodecyl sulfate to
1% and proteinase K to 200 ug ml-1 were added to the sample and incubated at
37 degrees celsius for 30 min and then at 55 degrees celsius for 30 min. The
lysates were extracted with an equal volume of
phenol:isoamylalcohol:chloroform (25:1:24) followed by two subsequent equal
volumes of isoamylalcohol:chloroform (1:24). The DNA was purified by
precipitation using sodium acetate (3M) and isopropanol (100%) for at least 1
hour at -20oC and centrifuged at room temperature for 30 min at 20,000 x g.
The resulting pellet was washed with 80% ethanol, vortexed for 30 s and
centrifuged at 16,000 x g for 10 min. The pellet was dried and stored at
-20C.\\u00a0 (See below for Microbial Processing description.)
 
Seawater samples were analyzed for macronutrients (nitrate + nitrite, nitrite,
ammonium, ortho phosphate, and silicic acid)\\u00a0 at Oregon State University
using a continuous segmented flow system consisting of a Technicon
AutoAnalyzer II (SEAL Analytical) and an Alpkem RFA 300 Rapid Flow Analyzer
(Alpkem) as conducted previously (Apprill and Rapp\\u00e9 2011). DOC was
determined via high temperature combustion on a modified Shimadzu TOC-V
(Shimadzu Scientific Instruments, Columbia, MD) (Carlson et al. 2010). Flow
cytometry was performed on 1 ml seawater preserved to a final concentration of
4% paraformaldehyde to enumerate pigmented picoeukaryotes, Synechococcus, and
non-pigmented picoplankton using methods described in Apprill and Rapp\\u00e9
(2011). High and low DNA-containing cells were enumerated following SybrGreen
staining. The ANOVA and Tukey\\u2019s HSD statistics were conducted as
described below.";
    String awards_0_award_nid "564441";
    String awards_0_award_number "OCE-1233612";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1233612";
    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 "Dr David  L. Garrison";
    String awards_0_program_manager_nid "50534";
    String cdm_data_type "Other";
    String comment 
"Bacterioplankton data from aquaria experiments 
 A. Apprill, PI 
 Version 29 July 2016 
  
   Columns Measured with Flow Cytometry: 
 	  nonPigmentPico,synechococcus,picoeukaryote, 
 	  lowHeterotrophicBac, and highHeterotrophicBac 
  
   Columns Measured with FISH: 
 	  SAR11,rhodobacteracea,alteromonas,vibrio, 
 	  thaumarchaeota, and euryarchaeota 
  
   Column Units: 
 	  Temperature: Celsius 
 	  Salinity: PPT 
 	  Flow Cytometry and FISH: cells per mL 
 	  DAPI counts: cells per mL 
 	  Growth and Grazing: day -1 
 	  Nutrients: micromoles";
    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 2.2d  13 Jun 2019";
    String date_created "2016-07-29T13:07:47Z";
    String date_modified "2019-06-05T18:00:55Z";
    String defaultDataQuery "&time";
    String doi "10.1575/1912/bco-dmo.652849.1";
    String history 
"2019-07-21T00:34:28Z (local files)
2019-07-21T00:34:28Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_652849.html";
    String infoUrl "https://www.bco-dmo.org/dataset/652849";
    String institution "BCO-DMO";
    String instruments_0_dataset_instrument_description "Slides were enumerated using this microscope.";
    String instruments_0_dataset_instrument_nid "652874";
    String instruments_0_description "Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB06/";
    String instruments_0_instrument_name "Microscope-Fluorescence";
    String instruments_0_instrument_nid "695";
    String instruments_0_supplied_name "AX70 epifluorescent microscope";
    String instruments_1_acronym "Thermal Cycler";
    String instruments_1_dataset_instrument_description "Reactions carried out on a Bio-Rad thermocycler.";
    String instruments_1_dataset_instrument_nid "652875";
    String instruments_1_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_1_instrument_name "PCR Thermal Cycler";
    String instruments_1_instrument_nid "471582";
    String instruments_1_supplied_name "Bio-Rad thermocycler";
    String keywords "accession, accession_number, alteromonas, ammonia, ammonium, bac, bacGrazing_coefficient_mean, bacGrowth_constant_mean, bco, bco-dmo, biological, chemical, chemistry, coefficient, commerce, concentration, constant, count, dapi, DAPI_count, data, dataset, days, density, department, description, dissolved, dissolved nutrients, dmo, doc, earth, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Salinity/Density > Salinity, erddap, euryarchaeota, grazing, growth, heterotrophic, high, highHeterotrophicBac, low, lowHeterotrophicBac, management, mean, mesocosm, mole, mole_concentration_of_ammonium_in_sea_water, n02, n03, N03_N02, name, nh4, non, nonPigmentPico, number, nutrients, ocean, oceanography, oceans, office, p04, pico, picoeukaryote, pigment, practical, preliminary, rhodobacteracea, rhodobacteraceaGrazing_coefficient, rhodobacteraceaGrowth_constant_mean, salinity, sar11, SAR11Grazing_coefficient, SAR11Growth_constant_mean, science, sea, sea_water_practical_salinity, seawater, si04, statistics, synechococcus, synechococcusGrazing_coefficient, synechococcusGrowth_constant_mean, tank, temperature, thaumarchaeota, time, timepoint, timepoint_days, timepoint_name, treatment, treatment_description, vibrio, water";
    String keywords_vocabulary "GCMD Science Keywords";
    String license 
"The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.";
    String metadata_source "https://www.bco-dmo.org/api/dataset/652849";
    String param_mapping "{'652849': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/652849/parameters";
    String people_0_affiliation "Woods Hole Oceanographic Institution";
    String people_0_affiliation_acronym "WHOI";
    String people_0_person_name "Dr Amy Apprill";
    String people_0_person_nid "553489";
    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 "Fundamental Coral-Microbial Associations";
    String projects_0_acronym "Coral Microbial Relationships";
    String projects_0_description 
"Description from NSF award abstract:
Reef-building corals are in decline worldwide due in part to climate change and other human activities, and it is becoming increasingly important to understand what aspects of coral biology are degraded by environmental stress which then leads to coral mortality. It is now widely known that corals harbor communities of bacteria and archaea that are believed to play important roles in maintaining the health of their hosts, but we lack any appreciable understanding about the identity of the microbial associates regularly residing within healthy, reef-building corals. This project asks the central question: do reef-building corals harbor fundamental or persistent microbial associates that are symbiotic within their tissues? In order to address this hypothesis, the investigator will assess the identity of the bacterial and archaeal microbes using a variety of molecular and microscopy approaches that includes the identification and localization of a widespread group of coral bacterial associates belonging to the genus Endozoicomonas. The results of this study will then be used to develop additional questions about the role of these microbial associates in nutrient cycling and how they contribute to the health and survival of corals.";
    String projects_0_end_date "2016-08";
    String projects_0_geolocation "Florida Keys, Federated States of Micronesia, Red Sea, & Bermuda";
    String projects_0_name "Fundamental Coral-Microbial Associations";
    String projects_0_project_nid "564442";
    String projects_0_start_date "2012-09";
    String publisher_name "Hannah Ake";
    String publisher_role "BCO-DMO Data Manager(s)";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v29";
    String summary "Bacterioplankton data from coral and coral mucus aquaria experiments conducted at Bermuda Institute of Ocean Sciences in 2013";
    String title "Bacterioplankton data from coral and coral mucus aquaria experiments conducted at Bermuda Institute of Ocean Sciences in 2013";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.5-beta";
  }
}

 

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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