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 Sediment cores were retrieved from bioturbated, intertidal sediments at low\ntide with a 7.5 cm (inner diameter) clear Plexiglas liner by pushing it\ndirectly into the sediment with minimum pressure as not to artificially force\nthe sediment horizons together. The end of the core (i.e., the deepest\nhorizon) was plugged with a rubber stopper and the sediment core was placed on\nice. Typical transport back to the laboratory for pore water extraction was\n0.5 hours. Sediment temperature and bottom water salinity were recorded at the\ntime of sampling with an alcohol thermometer and refractometer, respectively.\n \nOnce back to the laboratory, the cores were removed from ice and 5 cm Rhizons\n(0.16-0.19 um pore size) were inserted into pre-drilled 7 mm holes at 1 cm\ndepth intervals to a depth of 10 cm. Pore waters were extracted by pulling\nnegative pressure on the Rhizon with a 10 mL sterile syringe and holding the\nsyringe plunger in place with a small wooden block placed between the syringe\nbody and the plunger. Once pore water was extracted in the syringe, it was\nremoved from the Rhizon, dispensed into a 15 mL centrifuge tube, and 250 uL of\npore water was immediately transferred to 250 uL of Ferrozine buffer (10 mM in\n50 mM HEPES buffer) and read on a MultiSkan MCC plate reader at 562 nm\nabsorbance. The sediment core was then extruded and sliced into 1 cm intervals\nand dried in an oven at 70-80 degrees C for 24 hours, and then poorly-\ncrystalline iron oxides (i.e., ferrihydrite and lepidocrocite) were extracted\nwith 1 M hydroxylamine HCl in 25 % acetic acid (v/v) for 48 hours on a\nrotating shaker at 200 rpm. The extractions were allowed to settle for a few\nhours, then 10 uL was diluted into 990 uL (1:100 dilution) of distilled water\ncontaining 100 uL of Ferrozine buffer. The samples were read as above at 562\nnm on the Multiskan MCC plate reader.\n \nNote: data were not collected for months of August and October .
attribute NC_GLOBAL awards_0_award_nid String 544591
attribute NC_GLOBAL awards_0_award_number String OCE-1459600
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_1_award_nid String 626092
attribute NC_GLOBAL awards_1_award_number String OCE-1459252
attribute NC_GLOBAL awards_1_data_url String http://www.nsf.gov/awardsearch/showAward?AWD_ID=1459252 (external link)
attribute NC_GLOBAL awards_1_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_1_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_1_funding_source_nid String 355
attribute NC_GLOBAL awards_1_program_manager String David L. Garrison
attribute NC_GLOBAL awards_1_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Seasonal iron biogeochemistry \n  PI: David Emerson (Bigelow Laboratory for Ocean Sciences) \n  Co-PI: Peter Girguis (Harvard University) \n  Contact: Jacob Beam (Bigelow Laboratory for Ocean Sciences) \n  Version date: 01 June 2018
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 date_created String 2018-06-01T19:12:56Z
attribute NC_GLOBAL date_modified String 2019-03-15T18:25:03Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.737962.1
attribute NC_GLOBAL Easternmost_Easting double -69.648632
attribute NC_GLOBAL geospatial_lat_max double 43.994827
attribute NC_GLOBAL geospatial_lat_min double 43.994827
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -69.648632
attribute NC_GLOBAL geospatial_lon_min double -69.648632
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 9.5
attribute NC_GLOBAL geospatial_vertical_min double 0.5
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/737962 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Refractometer
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 737976
attribute NC_GLOBAL instruments_0_description String A refractometer is a laboratory or field device for the measurement of an index of refraction (refractometry). The index of refraction is calculated from Snell's law and can be calculated from the composition of the material using the Gladstone-Dale relation.\n\nIn optics the refractive index (or index of refraction) n of a substance (optical medium) is a dimensionless number that describes how light, or any other radiation, propagates through that medium.
attribute NC_GLOBAL instruments_0_instrument_name String Refractometer
attribute NC_GLOBAL instruments_0_instrument_nid String 679
attribute NC_GLOBAL instruments_0_supplied_name String Handheld salinity refractometer with temperature compensation (Marine Depot)
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 737977
attribute NC_GLOBAL instruments_1_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_1_instrument_name String plate reader
attribute NC_GLOBAL instruments_1_instrument_nid String 528693
attribute NC_GLOBAL instruments_1_supplied_name String MultiSkan MCC plate reader
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 737974
attribute NC_GLOBAL instruments_2_description String Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.\n\nDescription obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/
attribute NC_GLOBAL instruments_2_instrument_name String Push Corer
attribute NC_GLOBAL instruments_2_instrument_nid String 628287
attribute NC_GLOBAL instruments_3_dataset_instrument_nid String 737975
attribute NC_GLOBAL instruments_3_instrument_name String Thermometer
attribute NC_GLOBAL instruments_3_instrument_nid String 725867
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, chemical, crystalline, data, dataset, date, density, depth, dmo, earth, Earth Science > Oceans > Salinity/Density > Salinity, erddap, ferrous, ferrous_iron, iron, latitude, longitude, management, ocean, oceanography, oceans, office, oxide, poorly, poorly_crystalline_iron_oxide, practical, preliminary, salinity, science, sea, sea_water_practical_salinity, seawater, sed, sed_temp, site, temperature, water
attribute NC_GLOBAL keywords_vocabulary String GCMD Science Keywords
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/737962/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/737962 (external link)
attribute NC_GLOBAL Northernmost_Northing double 43.994827
attribute NC_GLOBAL param_mapping String {'737962': {'lat': 'flag - latitude', 'depth': 'flag - depth', 'long': 'flag - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/737962/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Bigelow Laboratory for Ocean Sciences
attribute NC_GLOBAL people_0_person_name String David Emerson
attribute NC_GLOBAL people_0_person_nid String 544585
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 Harvard University
attribute NC_GLOBAL people_1_person_name String Peter Girguis
attribute NC_GLOBAL people_1_person_nid String 544586
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String Bigelow Laboratory for Ocean Sciences
attribute NC_GLOBAL people_2_person_name String Jacob Beam
attribute NC_GLOBAL people_2_person_nid String 737970
attribute NC_GLOBAL people_2_role String Contact
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL people_3_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_3_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_3_person_name String Shannon Rauch
attribute NC_GLOBAL people_3_person_nid String 51498
attribute NC_GLOBAL people_3_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL project String SedimentaryIronCycle
attribute NC_GLOBAL projects_0_acronym String SedimentaryIronCycle
attribute NC_GLOBAL projects_0_description String Iron is a critical element for life that serves as an essential trace element for eukaryotic organisms. It is also able to support the growth of a cohort of microbes that can either gain energy for growth via oxidation of ferrous (Fe(II)) to ferric (Fe(III)) iron, or by utilizing Fe(III) for anaerobic respiration coupled to oxidation of simple organic matter or H2. This coupled process is referred to as the microbial iron cycle. One of the primary sources of iron to the ocean comes from dissolved iron (dFe) that is produced through oxidation and reduction processes in the sediment where iron is abundant. The dFe is transported into the overlaying water where it is an essential nutrient for phytoplankton responsible for primary production in the world’s oceans. In fact, iron limitation significantly impacts production in as much as a third of the world’s open oceans. The basic geochemistry of this process is understood; however important gaps exist in our knowledge about the details of how the iron cycle works, and how critical a role bacteria play in it.\nIntellectual Merit. Conventional wisdom holds that most of the iron oxidation in sediments is abiological, as a result of the rapid kinetics of chemical iron oxidation in the presence of oxygen. This proposal aims to question this conventional view and enhance our understanding of the microbes involved in the sedimentary iron cycle, with an emphasis on the bacteria that catalyze the oxidation of iron. These Fe-oxidizing bacteria (FeOB) utilize iron as a sole energy source for growth, and are autotrophic.  They were only discovered in the ocean about forty-five years ago, and are now known to be abundant at hydrothermal vents that emanate ferrous-rich fluids. More recently, the first evidence was published that they could inhabit coastal sediments, albeit at reduced numbers, and even be abundant in some continental shelf sediments. These habitats are far removed from hydrothermal vents, and reveal the sediments may be an important habitat for FeOB that live on ferrous iron generated in the sediment. This begs the question: are FeOB playing an important role in the oxidative part of the sedimentary Fe-cycle? One important attribute of FeOB is their ability to grow at very low levels of O2, an essential strategy for them to outcompete chemical iron oxidation. How low a level of O2 can sustain them, and how this might affect their distribution in sediments is unknown. In part, this is due to the technical challenges of measuring O2 concentrations and dynamics at very low levels; yet these concentrations could be where FeOB flourish. The central hypothesis of this proposal is that FeOB are more common in marine sedimentary environments than previously recognized, and play a substantive role in governing the iron flux from the sediments into the water column by constraining the release of dFe from sediments. A set of experimental objectives are proposed to test this. A survey of near shore regions in the Gulf of Maine, and a transect along the Monterey Canyon off the coast of California will obtain cores of sedimentary muds and look at the vertical distribution of FeOB and putative Fe-reducing bacteria using sensitive techniques to detect their presence and relative abundance. Some of these same sediments will be used in a novel reactor system that will allow for precise control of O2 levels and iron concentration to measure the dynamics of the iron cycle under different oxygen regimens. Finally pure cultures of FeOB with different O2 affinities will be tested in a bioreactor coupled to a highly sensitive mass spectrometer to determine the lower limits of O2 utilization for different FeOB growing on iron, thus providing mechanistic insight into their activity and distribution in low oxygen environments.\nBroader Impacts. An important impact of climate change on marine environments is a predicted increase in low O2 or hypoxic zones in the ocean. Hypoxia in association with marine sediments will have a profound influence on the sedimentary iron cycle, and is likely to lead to greater inputs of dFe into the ocean. In the longer term, this increase in dFe flux could alleviate iron-limitation in some regions of the ocean, thereby enhancing the rate of CO2-fixation and draw down of CO2 from the atmosphere. This is one important reason for developing a better understanding of microbial control of sedimentary iron cycle. This project will also provide training to a postdoctoral scientist, graduate students and undergraduates. This project will contribute to a student initiated exhibit, entitled ‘Iron and the evolution of life on Earth’ at the Harvard Museum of Natural History providing a unique opportunity for undergraduate training and outreach.
attribute NC_GLOBAL projects_0_geolocation String Intertidal coastal river and coastal shelf sediments, mid-coast, Maine, USA; Monteray Bay Canyon, sediments, CA, USA
attribute NC_GLOBAL projects_0_name String Collaborative Research: The Role of Iron-oxidizing Bacteria in the Sedimentary Iron Cycle: Ecological, Physiological and Biogeochemical Implications
attribute NC_GLOBAL projects_0_project_nid String 544584
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 43.994827
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String site,latitude,longitude
attribute NC_GLOBAL summary String Pore water and solid phase iron geochemical data from a coastal Maine intertidal mudflat from November 2015 to November 2016.
attribute NC_GLOBAL title String [Seasonal iron biogeochemistry] - Pore water and solid phase iron geochemical data from a coastal Maine intertidal mudflat from November 2015 to November 2016 (Collaborative Research: The Role of Iron-oxidizing Bacteria in the Sedimentary Iron Cycle: Ecological, Physiological and Biogeochemical Implications)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -69.648632
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable site String
attribute site bcodmo_name String site
attribute site description String Name of sampling site
attribute site long_name String Site
attribute site units String unitless
variable latitude double
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 43.994827, 43.994827
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 of sampling site
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 -69.648632, -69.648632
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 of sampling site
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 source_name String long
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable date int
attribute date _FillValue int 2147483647
attribute date actual_range int 20151118, 20161109
attribute date bcodmo_name String date
attribute date description String Date of sampling; formatted as yyyymmdd
attribute date long_name String Date
attribute date nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute date 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 0.5, 9.5
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 Sampling depth
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 sed_temp float
attribute sed_temp _FillValue float NaN
attribute sed_temp actual_range float 0.5, 21.0
attribute sed_temp bcodmo_name String temperature
attribute sed_temp description String Sediment temperature
attribute sed_temp long_name String Sed Temp
attribute sed_temp units String degrees Celsius
variable salinity float
attribute salinity _FillValue float NaN
attribute salinity actual_range float 19.5, 37.0
attribute salinity bcodmo_name String sal
attribute salinity colorBarMaximum double 37.0
attribute salinity colorBarMinimum double 32.0
attribute salinity description String Low tide surface water salinity
attribute salinity long_name String Sea Water Practical Salinity
attribute salinity nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/ (external link)
attribute salinity units String practical salinity units
variable ferrous_iron short
attribute ferrous_iron _FillValue short 32767
attribute ferrous_iron actual_range short 0, 272
attribute ferrous_iron bcodmo_name String Fe
attribute ferrous_iron description String Dissolved pore water ferrous iron
attribute ferrous_iron long_name String Ferrous Iron
attribute ferrous_iron units String micromoles per liter (umol/L)
variable poorly_crystalline_iron_oxide short
attribute poorly_crystalline_iron_oxide _FillValue short 32767
attribute poorly_crystalline_iron_oxide actual_range short 41, 380
attribute poorly_crystalline_iron_oxide bcodmo_name String Fe
attribute poorly_crystalline_iron_oxide description String Sedimentary poorly-crystalline iron oxide Fe
attribute poorly_crystalline_iron_oxide long_name String Poorly Crystalline Iron Oxide
attribute poorly_crystalline_iron_oxide units String micromoles per gram dry sediment (umol/g)

 
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