BCO-DMO ERDDAP
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Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson
attribute NC_GLOBAL acquisition_description String Alkaline phosphatase (AP) activity was measured using the fluorogenic\nsubstrate 4-methylumbelliferyl phosphate (MUF-P) (Sigma-Aldrich, St. Louis,\nMO) and its reference standard, methylumbelliferone (MUF). Fluorescence was\nmeasured using black, flat bottom, 96-well microplates in a Spark 10M\nMultimode Microplate Reader (Tecan, M\\u00e4nnedorf, Switzerland). Fluorescence\nof MUF is greatest at pH 10, therefore 25 \\u03bcL of 0.4 M NaOH was added to\nthe wells (final concentration 40 mM) to be read. 25 \\u03bcL of 1M EDTA was\nadded as well (100 mM final concentration) to prevent precipitation of c 439\narbonate from sampled veins.\n \nFluorescence was measured with an excitation wavelength of 380 nm and emission\nof 454 nm for all substrates and standards. One cm3 powdered rock was mixed\nwith 5 cm3 of sterileartificial seawater (ASW) in a 8 mL serum vial with\n90:5:5 N2:CO2:H2 headspace. 700 \\u03bcL of each slurry was withdrawn with a\nsterile syringe to a 1.5 mL Eppendorf tube after setup but before sealing the\nvial; this sample served as T0, with triplicate 200 \\u03bcL technical\nreplicates. These 700 \\u03bcL samples were briefly centrifuged (60 sec. at\n2500 rpm) and the supernatant used for the T0 analyses.\n \nTwo additional samples were taken using the same methods as for T0 after at\nleast 2 weeks and then again after 4-6 weeks to generate a slope of activity.\nIncubations were kept at 10\\u02daC, the inferred in situ temperature, for the\nduration of each assay. Autoclaved, powderized rock from each of the samples\nwas tested to determine the amount of fluorophore adsorbance to rock powder.\n \nAdsorbance was found to behave in a systematic manner, resulting in a straight\nline when comparing fluorescence standards in artificial seawater (ASW) alone\nwith fluorescence standards plus rock powder in ASW, although this\nrelationship was found to be different when measured at 4 hours versus days\nlater. Therefore, a correction factor for adsorbance was applied to the enzyme\ndata for the initial measurement (t0, y=1.90x-676), taken <2 hours after\nexperiment initiation, versus the second and third measurements (t1 and t2, y\n= 4.64x - 303), taken days to weeks later. Negative controls consisting of the\nsame ASW used for the sample incubations plus substrate, but no sample, were\nconsistently below detection. The limit of quantification for the AP assay,\ndefined as 3X the standard deviation of the blank, was 0.0242 pmol cm-3 rock\nhour-1 based on analysis of eight blanks.
attribute NC_GLOBAL awards_0_award_nid String 709555
attribute NC_GLOBAL awards_0_award_number String OCE-1658031
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1658031 (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 David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Supplementary Table 3B: Cell counts \n  PI: Virginia Edgcomb  \n  Data Version 1: 2020-06-22
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 2020-05-14T15:59:17Z
attribute NC_GLOBAL date_modified String 2020-07-08T20:35:34Z
attribute NC_GLOBAL defaultDataQuery String &amp;time&lt;now
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.811483.1
attribute NC_GLOBAL Easternmost_Easting double 57.278183
attribute NC_GLOBAL geospatial_lat_max double -32.70567
attribute NC_GLOBAL geospatial_lat_min double -32.70567
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double 57.278183
attribute NC_GLOBAL geospatial_lon_min double 57.278183
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 747.7
attribute NC_GLOBAL geospatial_vertical_min double 10.7
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/811483 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Cell counts performed with a Zeiss Axio Imager M2 Epifluorescence microscope.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 813402
attribute NC_GLOBAL instruments_0_description String 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.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB06/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Microscope-Fluorescence
attribute NC_GLOBAL instruments_0_instrument_nid String 695
attribute NC_GLOBAL instruments_0_supplied_name String Zeiss Axio Imager M2 Epifluorescence microscope
attribute NC_GLOBAL instruments_1_acronym String sonicator
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Cell separation was performed through sonication with Diagenode Bioruptor sonication device.
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 813403
attribute NC_GLOBAL instruments_1_description String Instrument that applies sound energy to agitate particles in a sample.
attribute NC_GLOBAL instruments_1_instrument_name String ultrasonic cell disrupter
attribute NC_GLOBAL instruments_1_instrument_nid String 528691
attribute NC_GLOBAL instruments_1_supplied_name String Diagenode Bioruptor
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Alkaline Phosphate activity was measured with a Spark 10M Multimode Microplate Reader (Tecan, Männedorf, Switzerland).
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 813418
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 Spark 10M Multimode Microplate Reader
attribute NC_GLOBAL keywords String activity, AP_activity, average, bco, bco-dmo, biological, chemical, data, dataset, depth, deviation, dmo, erddap, latitude, longitude, management, measurment, oceanography, office, preliminary, replicate, Replicate_1, Replicate_2, sample, standard, Standard_Deviation, time, Time_of_AP_measurment
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/811483/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/811483 (external link)
attribute NC_GLOBAL Northernmost_Northing double -32.70567
attribute NC_GLOBAL param_mapping String {'811483': {'Latitude': 'flag - latitude', 'Depth': 'flag - depth', 'Longitude': 'flag - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/811483/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_0_affiliation_acronym String WHOI
attribute NC_GLOBAL people_0_person_name String Virginia P. Edgcomb
attribute NC_GLOBAL people_0_person_nid String 51284
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
attribute NC_GLOBAL people_1_person_name String Virginia P. Edgcomb
attribute NC_GLOBAL people_1_person_nid String 51284
attribute NC_GLOBAL people_1_role String Contact
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL people_2_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Karen Soenen
attribute NC_GLOBAL people_2_person_nid String 748773
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL project String Subseafloor Lower Crust Microbiology
attribute NC_GLOBAL projects_0_acronym String Subseafloor Lower Crust Microbiology
attribute NC_GLOBAL projects_0_description String NSF abstract:\nThe lower ocean crust has remained largely unexplored and represents one of the last frontiers for biological exploration on Earth. Preliminary data indicate an active subsurface biosphere in samples of the lower oceanic crust collected from Atlantis Bank in the SW Indian Ocean as deep as 790 m below the seafloor. Even if life exists in only a fraction of the habitable volume where temperatures permit and fluid flow can deliver carbon and energy sources, an active lower oceanic crust biosphere would have implications for deep carbon budgets and yield insights into microbiota that may have existed on early Earth. This is all of great interest to other research disciplines, educators, and students alike. A K-12 education program will capitalize on groundwork laid by outreach collaborator, A. Martinez, a 7th grade teacher in Eagle Pass, TX, who sailed as outreach expert on Drilling Expedition 360. Martinez works at a Title 1 school with ~98% Hispanic and ~2% Native American students and a high number of English Language Learners and migrants. Annual school visits occur during which the project investigators present hands on-activities introducing students to microbiology, and talks on marine microbiology, the project, and how to pursue science related careers. In addition, monthly Skype meetings with students and PIs update them on project progress. Students travel to the University of Texas Marine Science Institute annually, where they get a campus tour and a 3-hour cruise on the R/V Katy, during which they learn about and help with different oceanographic sampling approaches. The project partially supports two graduate students, a Woods Hole undergraduate summer student, the participation of multiple Texas A+M undergraduate students, and 3 principal investigators at two institutions, including one early career researcher who has not previously received NSF support of his own.\nGiven the dearth of knowledge of the lower oceanic crust, this project is poised to transform our understanding of life in this vast environment. The project assesses metabolic functions within all three domains of life in this crustal biosphere, with a focus on nutrient cycling and evaluation of connections to other deep marine microbial habitats. The lower ocean crust represents a potentially vast biosphere whose microbial constituents and the biogeochemical cycles they mediate are likely linked to deep ocean processes through faulting and subsurface fluid flow. Atlantis Bank represents a tectonic window that exposes lower oceanic crust directly at the seafloor. This enables seafloor drilling and research on an environment that can transform our understanding of connections between the deep subseafloor biosphere and the rest of the ocean. Preliminary analysis of recovered rocks from Expedition 360 suggests the interaction of seawater with the lower oceanic crust creates varied geochemical conditions capable of supporting diverse microbial life by providing nutrients and chemical energy. This project is the first interdisciplinary investigation of the microbiology of all 3 domains of life in basement samples that combines diversity and \"meta-omics\" analyses, analysis of nutrient addition experiments, high-throughput culturing and physiological analyses of isolates, including evaluation of their ability to utilize specific carbon sources, Raman spectroscopy, and lipid biomarker analyses. Comparative genomics are used to compare genes and pathways relevant to carbon cycling in these samples to data from published studies of other deep-sea environments. The collected samples present a rare and time-sensitive opportunity to gain detailed insights into microbial life, available carbon and energy sources for this life, and of dispersal of microbiota and connections in biogeochemical processes between the lower oceanic crust and the overlying aphotic water column.\nAbout the study area:\nThe International Ocean Discovery Program (IODP) Expedition 360 explored the lower crust at Atlantis Bank, a 12 Ma oceanic core complex on the ultraslow-spreading SW Indian Ridge. This oceanic core complex represents a tectonic window that exposes lower oceanic crust and mantle directly at the seafloor, and the expedition provided an unprecedented opportunity to access this habitat in the Indian Ocean.
attribute NC_GLOBAL projects_0_end_date String 2020-01
attribute NC_GLOBAL projects_0_geolocation String SW Indian Ridge, Indian Ocean
attribute NC_GLOBAL projects_0_name String Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches
attribute NC_GLOBAL projects_0_project_nid String 709556
attribute NC_GLOBAL projects_0_start_date String 2017-02
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 Southernmost_Northing double -32.70567
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String latitude,longitude
attribute NC_GLOBAL summary String Supplementary Table 3B: Overview of archaeal and bacterial lipid biomarkers and cell counts. Replicate cell counts for the 11 samples and alkaline phosphatase activity measurements available for any of the 11 samples. Samples were taken on board of the JOIDES Resolution  between November 30, 2015 and January 30, 2016 in the SW Indian Ridge.
attribute NC_GLOBAL title String [IODP360 - Replicate Cell Counts] - Supplementary Table 3B: Replicate cell counts for the 11 samples and alkaline phosphatase activity measurements available for any of the 11 samples (Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double 57.278183
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5
variable Sample String
attribute Sample bcodmo_name String sample
attribute Sample description String Sample ID
attribute Sample long_name String Sample
attribute Sample nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Sample units String unitless
variable latitude double
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double -32.70567, -32.70567
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String Latitude, south is negative
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude double
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double 57.278183, 57.278183
attribute longitude axis String X
attribute longitude bcodmo_name String longitude
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String Longitude, west is negative
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable depth double
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 10.7, 747.7
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 Depth below seafloor
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 Replicate_1 float
attribute Replicate_1 _FillValue float NaN
attribute Replicate_1 actual_range float 8.77, 3000.0
attribute Replicate_1 bcodmo_name String replicate
attribute Replicate_1 description String Replicate 1
attribute Replicate_1 long_name String Replicate 1
attribute Replicate_1 units String cells per cubic centimeter (cells/cm3)
variable Replicate_2 float
attribute Replicate_2 _FillValue float NaN
attribute Replicate_2 actual_range float 17.5, 1740.0
attribute Replicate_2 bcodmo_name String replicate
attribute Replicate_2 description String Replicate 2
attribute Replicate_2 long_name String Replicate 2
attribute Replicate_2 units String cells per cubic centimeter (cells/cm3)
variable Average short
attribute Average _FillValue short 32767
attribute Average actual_range short 115, 1656
attribute Average bcodmo_name String mean
attribute Average description String Average number of cells
attribute Average long_name String Average
attribute Average units String cells per cubic centimeter (cells/cm3)
variable Standard_Deviation short
attribute Standard_Deviation _FillValue short 32767
attribute Standard_Deviation actual_range short 6, 1901
attribute Standard_Deviation bcodmo_name String standard deviation
attribute Standard_Deviation colorBarMaximum double 50.0
attribute Standard_Deviation colorBarMinimum double 0.0
attribute Standard_Deviation description String Standard deviation of average
attribute Standard_Deviation long_name String Standard Deviation
attribute Standard_Deviation units String cells per cubic centimeter (cells/cm3)
variable AP_activity float
attribute AP_activity _FillValue float NaN
attribute AP_activity actual_range float 0.04, 2.3
attribute AP_activity bcodmo_name String unknown
attribute AP_activity description String Alkaline Phosphatase activity
attribute AP_activity long_name String AP Activity
attribute AP_activity units String picomole per gram per hour (pmol g-1 h-1)
variable Time_of_AP_measurment short
attribute Time_of_AP_measurment _FillValue short 32767
attribute Time_of_AP_measurment actual_range short 876, 3053
attribute Time_of_AP_measurment bcodmo_name String incubation time
attribute Time_of_AP_measurment description String Time of Alkaline Phosphatase measurements
attribute Time_of_AP_measurment long_name String Time Of AP Measurment
attribute Time_of_AP_measurment nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/AZDRZZ01/ (external link)
attribute Time_of_AP_measurment units String hours (Hr)

 
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