BCO-DMO ERDDAP
Accessing BCO-DMO data 		log in    
Brought to you by BCO-DMO    
 
 
Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String Seawater was transferred to 20 L carboys that were rinsed three times with\nwater from the sampling depth and then filled with seawater from a single\nNiskin bottle, using silicone tubing that had been acid washed then rinsed\nwith distilled water prior to use. From each carboy, water was dispensed into\nsmaller glass containers that were cleaned and pre-rinsed three times with\nwater from the carboy prior to dispensing. This water was used to measure cell\ncounts, bacterial productivity, and the activities of polysaccharide\nhydrolases, peptidases, and glucosidases. A separate glass Duran bottle was\nfilled with seawater from the carboy and sterilized in an autoclave for 20-30\nminutes to serve as a killed control for microbial activity measurements.\n \nTwo substrates, -glucose and -glucose linked to a 4-methylumbelliferyl (MUF)\nfluorophore, were used to measure glucosidase activities. Five substrates\nlinked to a 7-amido-4-methyl coumarin (MCA) fluorophore, one amino acid \\u2013\nleucine \\u2013 and four oligopeptides \\u2013 the chymotrypsin substrates\nalanine-alanine-phenylalanine (AAF) and alanine-alanine-proline-phenylalanine\n(AAPF), and the trypsin substrates glutamine-alanine-arginine (QAR) and\nphenylalanine-serine-arginine (FSR) \\u2013 were used to measure exo- and endo-\nacting peptidase activities, respectively. Hydrolysis rates of the substrates\nwere measured as an increase in fluorescence as the fluorophore was hydrolyzed\nfrom the substrate over time [as in Hoppe, 1993; Obayashi and Suzuki, 2005].\nIncubations with the seven low molecular weight substrates were set up in a\n96-well plate. For each substrate, triplicate wells were filled with a total\nvolume of 200 L seawater for experimental incubations; triplicate wells were\nfilled with 200 L autoclaved seawater for killed control incubations.\nSubstrate was added at saturating concentrations. A saturation curve was\ndetermined with surface water from each station to determine saturating\nconcentrations of substrate. The saturating concentration was identified as\nthe lowest tested concentration of substrate at which additional substrate did\nnot yield higher rates of hydrolysis. Fluorescence was measured over 24-48\nhours incubation time with a plate reader (TECAN spectrafluor plus; 360 nm\nexcitation, 460 emission), with time points taken every 4-6 hours. Hydrolysis\nrates were calculated from the rate of increase of fluorescence in the\nincubation over time relative to a set of standards of known concentration of\nfluorophore. Scripts to calculate hydrolysis rates and produce the figures\nshown here are available in the associated Github repository [Hoarfrost,\n2017].\n \nThe potential of the seawater microbial community to hydrolyze six high-\nmolecular-weight polysaccharides (arabinogalactan, chondroitin sulfate,\nfucoidan, laminarin, pullulan, and xylan) was investigated in surface and\nbottom water. For each substrate, three 50 mL falcon tubes were filled with\nseawater and one 50 mL falcon tube was filled with autoclaved seawater to\nserve as a killed control. Substrate was added at 3.5 \\u03bcM monomer-\nequivalent concentrations, except for fucoidan, which was added at 5 \\u03bcM\nconcentrations (a higher concentration was necessary for sufficient\nfluorescence signal). Two 50 mL falcon tubes \\u2013 one with seawater and one\nwith autoclaved seawater \\u2013 with no added substrate served as blank\ncontrols. Incubations were stored in the dark at as close to in situ\ntemperature as possible. Subsamples of the incubations were collected at time\nzero, and at six subsequent time points (t1-t6): 2 days, 5 days, 10 days, 17\ndays, 30 days, and 42 days. At each time point, 2 mL of seawater was collected\nfrom the 50 mL falcon tube using a sterile syringe, filtered through a 0.2\n\\u03bcm pore size syringe filter, and stored frozen until processing.
attribute NC_GLOBAL awards_0_award_nid String 712358
attribute NC_GLOBAL awards_0_award_number String OCE-1332881
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1332881 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Henrietta N Edmonds
attribute NC_GLOBAL awards_0_program_manager_nid String 51517
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Hydrolysis rates from bulk samples, plate reader results: EN556 \n   C. Arnosti (UNC) \n   version: 2017-11-16
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3  19 Dec 2019
attribute NC_GLOBAL dataset_current_state String Final and no updates
attribute NC_GLOBAL date_created String 2017-11-17T15:23:29Z
attribute NC_GLOBAL date_modified String 2020-05-13T14:03:00Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.719487.1
attribute NC_GLOBAL geospatial_vertical_max double 4574.0
attribute NC_GLOBAL geospatial_vertical_min double 1.0
attribute NC_GLOBAL geospatial_vertical_positive String down
attribute NC_GLOBAL geospatial_vertical_units String m
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/719487 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Niskin bottle
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Used to collect water for large volume mesocosm experiments
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 719493
attribute NC_GLOBAL instruments_0_description String A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Niskin bottle
attribute NC_GLOBAL instruments_0_instrument_nid String 413
attribute NC_GLOBAL instruments_0_supplied_name String 30 liter Niskin bottles
attribute NC_GLOBAL instruments_1_acronym String Fluorometer
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 719494
attribute NC_GLOBAL instruments_1_description String A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/113/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Fluorometer
attribute NC_GLOBAL instruments_1_instrument_nid String 484
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 719495
attribute NC_GLOBAL instruments_2_description String Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: https://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.
attribute NC_GLOBAL instruments_2_instrument_name String plate reader
attribute NC_GLOBAL instruments_2_instrument_nid String 528693
attribute NC_GLOBAL instruments_2_supplied_name String TECAN spectrafluor plus
attribute NC_GLOBAL keywords String average, bco, bco-dmo, biological, cast, chemical, cruise, cruise_id, data, dataset, depth, depth_m, depth_no, dev, dmo, erddap, management, oceanography, office, preliminary, profiler, rate, rep1, rep1_rate, rep2, rep2_rate, rep3, rep3_rate, salinity, salinity-temperature-depth, station, std, std_dev, substrate, temperature
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/719487/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/719487 (external link)
attribute NC_GLOBAL param_mapping String {'719487': {'depth_m': 'master - depth'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/719487/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of North Carolina at Chapel Hill
attribute NC_GLOBAL people_0_affiliation_acronym String UNC-Chapel Hill
attribute NC_GLOBAL people_0_person_name String Carol Arnosti
attribute NC_GLOBAL people_0_person_nid String 661940
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Nancy Copley
attribute NC_GLOBAL people_1_person_nid String 50396
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Patterns of activities
attribute NC_GLOBAL projects_0_acronym String Patterns of activities
attribute NC_GLOBAL projects_0_description String NSF Award Abstract:\nHeterotrophic microbial communities are key players in the marine carbon cycle, transforming and respiring organic carbon, regenerating nutrients, and acting as the final filter in sediments through which organic matter passes before long-term burial. Microbially-driven carbon cycling in the ocean profoundly affects the global carbon cycle, but key factors determining rates and locations of organic matter remineralization are unclear. In this study, researchers from the University of North Carolina at Chapel Hill will investigate the ability of pelagic microbial communities to initiate the remineralization of polysaccharides and proteins, which together constitute a major pool of organic matter in the ocean. Results from this study will be predictive on a large scale regarding the nature of the microbial response to organic matter input, and will provide a mechanistic framework for interpreting organic matter reactivity in the ocean.\nBroader Impacts: This study will provide scientific training for undergraduate and graduate students from underrepresented groups. The project will also involve German colleagues, thus strengthening international scientific collaboration.
attribute NC_GLOBAL projects_0_end_date String 2017-07
attribute NC_GLOBAL projects_0_geolocation String Atlantic Ocean, Arctic Ocean, Pacific Ocean, Greenland
attribute NC_GLOBAL projects_0_name String Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?
attribute NC_GLOBAL projects_0_project_nid String 712359
attribute NC_GLOBAL projects_0_start_date String 2013-08
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String cruise_id
attribute NC_GLOBAL summary String This dataset includes polysaccharide hydrolysis rates to measure microbial enzyme activities and bacterial productivity, from bulk samples, plate reader results from RV/Endeavor EN556, 2015.
attribute NC_GLOBAL title String [EN556 bulk peptidase hydrolysis rates - plate reader] - Hydrolysis rates from bulk samples, plate reader results from RV/Endeavor EN556, 2015 (Patterns of activities project) (Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5
variable cruise_id String
attribute cruise_id bcodmo_name String cruise_id
attribute cruise_id description String cruise identifier
attribute cruise_id long_name String Cruise Id
attribute cruise_id units String unitless
variable station byte
attribute station _FillValue byte 127
attribute station actual_range byte 1, 8
attribute station bcodmo_name String station
attribute station description String station number
attribute station long_name String Station
attribute station units String unitless
variable cast byte
attribute cast _FillValue byte 127
attribute cast actual_range byte 1, 13
attribute cast bcodmo_name String cast
attribute cast description String cast number
attribute cast long_name String Cast
attribute cast units String unitless
variable depth_no String
attribute depth_no bcodmo_name String depth_comment
attribute depth_no description String depth description: sequence of depths sampled with 1 is surface and higher numbers at greater depths
attribute depth_no long_name String Depth
attribute depth_no standard_name String depth
attribute depth_no units String unitless
variable depth double
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 1.0, 4574.0
attribute depth axis String Z
attribute depth bcodmo_name String depth
attribute depth colorBarMaximum double 8000.0
attribute depth colorBarMinimum double -8000.0
attribute depth colorBarPalette String TopographyDepth
attribute depth description String actual depth at which water collected
attribute depth ioos_category String Location
attribute depth long_name String Depth
attribute depth nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/DEPH/ (external link)
attribute depth positive String down
attribute depth standard_name String depth
attribute depth units String m
variable substrate String
attribute substrate bcodmo_name String unknown
attribute substrate description String substrates for measurement of enzymatic activities: a-glu = alpha glucosidase: 4-methylumbelliferyl-a-D-glucopyranoside; b-glu = beta glucosidase: 4-methylumbelliferyl-beta-D-glucopyranoside; L = leucine aminopeptidase (L-leucine-7-amido-4 MCA); AAF = chymotrypsin activity: ala-ala-phe-MCA; AAPF = chymotrypsin activity: N-succinyl-ala-ala-pro-phe-MCA; QAR = trypsin activity: Boc-gln-ala-arg-MCA; FSR = trypsin activity: N-t-boc-phe-ser-arg-MCA
attribute substrate long_name String Substrate
attribute substrate units String unitless
variable rep1_rate float
attribute rep1_rate _FillValue float NaN
attribute rep1_rate actual_range float 0.0, 127.93
attribute rep1_rate bcodmo_name String unknown
attribute rep1_rate description String replicate 1 of enzymatic hydrolysis rate
attribute rep1_rate long_name String Rep1 Rate
attribute rep1_rate units String nanomol monosaccharide/liter/hour
variable rep2_rate float
attribute rep2_rate _FillValue float NaN
attribute rep2_rate actual_range float 0.0, 88.86
attribute rep2_rate bcodmo_name String unknown
attribute rep2_rate description String replicate 2 of enzymatic hydrolysis rate
attribute rep2_rate long_name String Rep2 Rate
attribute rep2_rate units String nanomol monosaccharide/liter/hour
variable rep3_rate float
attribute rep3_rate _FillValue float NaN
attribute rep3_rate actual_range float 0.0, 85.03
attribute rep3_rate bcodmo_name String unknown
attribute rep3_rate description String replicate 3 of enzymatic hydrolysis rate
attribute rep3_rate long_name String Rep3 Rate
attribute rep3_rate units String nanomol monosaccharide/liter/hour
variable average float
attribute average _FillValue float NaN
attribute average actual_range float 0.0, 80.0
attribute average bcodmo_name String unknown
attribute average description String average of the 3 hydrolysis rates
attribute average long_name String Average
attribute average units String nanomol monosaccharide/liter/hour
variable std_dev float
attribute std_dev _FillValue float NaN
attribute std_dev actual_range float 0.0, 53.23
attribute std_dev bcodmo_name String unknown
attribute std_dev description String standard deviation of the 3 hydrolysis rates
attribute std_dev long_name String Std Dev
attribute std_dev units String nanomol monosaccharide/liter/hour

 
ERDDAP, Version 2.22
Disclaimers | Privacy Policy | Contact