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 This study included cold seep and hydrothermal vent sediments from along the\nPacific coast of North America. Sediments were collected via 30 cm long\npolycarbonate pushcores from a cold methane seep at Hydrate Ridge\n(44\\u00b034'10. 20\\\"N, 125\\u00b0 8'48. 48\\\"W) at 777 m water depth with the\nROV Ropos (Dive 1458); hydrothermal vents at Guaymas Basin, Gulf of California\n(27\\u00b00'27.84\\\"N, 111\\u00b024'27.84\\\"W) at 2000 m with the DSV Alvin (Dive\n4486); and hydrothermal vents at Middle Valley, Juna de Fuca Ridge\n(48\\u00b027'26.40\\\"N, 128\\u00b042'30.60\\\"W) at 2413 m with the DSV Alvin (Dive\n4625). For this study, a total of three pushcores were collected from Hydrate\nRidge at 4\\u00b0C, one from Guaymas Basin at 30-35\\u00b0C, and one from Middle\nValley at 5\\u201357\\u00b0C (Table 4.1). Total genomic DNA was extracted using\na phenol-chloroform protocol modified to prevent nucleic acid loss and\neliminate potential inhibitors of downstream PCR, and which has been very\nsuccessful in studies of low biomass sediments (Adams et al. 2013). PCR\namplification was performed with primers designed to be universal to both\narchaea and bacteria (515F/806R) (Caporaso et al., 2012), containing attached\nIllumina adaptors and barcodes (Kozich et al., 2013). All DNA extracts were\namplified in duplicate with OmniTaq (Taq mutant) polymerase according to the\nmanufacturer\\u2019s instructions (DNA Polymerase Technologies, St. Louis, MO,\nUSA), with a final concentration of 0.2 \\u03bcM for each primer. For each PCR,\n1 \\u03bcL template DNA was added to the final reaction mixture for a final\nvolume of 50 \\u03bcl. Amplification conditions were as follows: 94\\u00b0C for\n3 min to denature DNA; 30 cycles at 94\\u00b0C for 45 s, 50\\u00b0C for 60 s,\nand 72\\u00b0C for 60 s; and a final extension of 10 min at 72 \\u00b0C.
attribute NC_GLOBAL awards_0_award_nid String 626092
attribute NC_GLOBAL awards_0_award_number String OCE-1459252
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward?AWD_ID=1459252 (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 Illumina Sequencing From Deep Sea Sediments \n  PI: Peter Girguis (Harvard) \n  Contributor: Melissa Adams \n  Version date: 12 October 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 2018-10-12T18:57:48Z
attribute NC_GLOBAL date_modified String 2019-03-15T18:04:04Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.747948.1
attribute NC_GLOBAL Easternmost_Easting double -111.4078
attribute NC_GLOBAL geospatial_lat_max double 48.45722
attribute NC_GLOBAL geospatial_lat_min double 27.0078
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -111.4078
attribute NC_GLOBAL geospatial_lon_min double -128.70861
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/747948 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Thermal Cycler
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 747953
attribute NC_GLOBAL instruments_0_description String 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.\n\n(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
attribute NC_GLOBAL instruments_0_instrument_name String PCR Thermal Cycler
attribute NC_GLOBAL instruments_0_instrument_nid String 471582
attribute NC_GLOBAL keywords String accession, analysis, Analysis_methods, bco, bco-dmo, biological, chemical, collected, data, dataset, description, description_of_the_types_of_sequences, dive, Dive_number, dmo, erddap, instrument, instrument_and_model, latitude, latitude_dms, link, locations, locations_where_species_were_collected, longitude, longitude_dms, management, methods, model, names, number, oceanography, office, preliminary, sequence, sequence_accession_number, sequences, sequencing, sequencing_and_analysis_methods, species, Species_Names, types, vessel, where
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/747948/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/747948 (external link)
attribute NC_GLOBAL Northernmost_Northing double 48.45722
attribute NC_GLOBAL param_mapping String {'747948': {'latitude': 'flag - latitude', 'longitude': 'flag - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/747948/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Harvard University
attribute NC_GLOBAL people_0_person_name String Peter Girguis
attribute NC_GLOBAL people_0_person_nid String 544586
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 Melissa Adams
attribute NC_GLOBAL people_1_person_nid String 747964
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 Shannon Rauch
attribute NC_GLOBAL people_2_person_nid String 51498
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 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 27.0078
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String Species_Names,description_of_the_types_of_sequences,sequencing_and_analysis_methods,instrument_and_model,Analysis_methods
attribute NC_GLOBAL summary String Illumina sequencing data (NCBI accession numbers) from sediment strata collected from the cold seeps of Hydrate Ridge, metalliferous sediments of Juan de Fuca Ridge, and organic-rich hydrothermal sediments of Guaymas Basin.
attribute NC_GLOBAL title String [Illumina Sequences] - Illumina sequencing data from sediment strata collected from the cold seeps of Hydrate Ridge, metalliferous sediments of Juan de Fuca Ridge, and organic-rich hydrothermal sediments of Guaymas Basin (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 -128.70861
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable sequence_accession_number String
attribute sequence_accession_number bcodmo_name String accession number
attribute sequence_accession_number description String NCBI accession number
attribute sequence_accession_number long_name String Sequence Accession Number
attribute sequence_accession_number units String unitless
variable link String
attribute link bcodmo_name String external_link
attribute link description String URL to NCBI accession
attribute link long_name String Link
attribute link units String unitless
variable Species_Names String
attribute Species_Names bcodmo_name String taxon
attribute Species_Names description String Description/name of species
attribute Species_Names long_name String Species Names
attribute Species_Names units String unitless
variable description_of_the_types_of_sequences String
attribute description_of_the_types_of_sequences bcodmo_name String sample_descrip
attribute description_of_the_types_of_sequences description String Description of the type of sequence
attribute description_of_the_types_of_sequences long_name String Description Of The Types Of Sequences
attribute description_of_the_types_of_sequences units String unitless
variable locations_where_species_were_collected String
attribute locations_where_species_were_collected bcodmo_name String site
attribute locations_where_species_were_collected description String Location of sample collection
attribute locations_where_species_were_collected long_name String Locations Where Species Were Collected
attribute locations_where_species_were_collected units String unitless
variable latitude_dms String
attribute latitude_dms bcodmo_name String latitude
attribute latitude_dms description String Latitude of sample collection in degrees, minutes, and seconds
attribute latitude_dms long_name String Latitude
attribute latitude_dms nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude_dms standard_name String latitude
attribute latitude_dms units String unitless
variable longitude_dms String
attribute longitude_dms bcodmo_name String longitude
attribute longitude_dms description String Longitude of sample collection in degrees, minutes, and seconds
attribute longitude_dms long_name String Longitude
attribute longitude_dms nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude_dms standard_name String longitude
attribute longitude_dms units String unitless
variable latitude double
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 27.0078, 48.45722
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 sample collection in decimal degrees; North = positive values
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 -128.70861, -111.4078
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 sample collection in degrees, minutes, and seconds; East = positive values
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 Vessel String
attribute Vessel bcodmo_name String instrument
attribute Vessel description String Name of collection vehicle
attribute Vessel long_name String Vessel
attribute Vessel units String unitless
variable Dive_number short
attribute Dive_number _FillValue short 32767
attribute Dive_number actual_range short 1458, 4625
attribute Dive_number bcodmo_name String dive_id
attribute Dive_number colorBarMaximum double 100.0
attribute Dive_number colorBarMinimum double 0.0
attribute Dive_number description String Dive ID number
attribute Dive_number long_name String Dive Number
attribute Dive_number units String unitless
variable sequencing_and_analysis_methods String
attribute sequencing_and_analysis_methods bcodmo_name String sampling_method
attribute sequencing_and_analysis_methods description String Description of sequencing and analysis methods
attribute sequencing_and_analysis_methods long_name String Sequencing And Analysis Methods
attribute sequencing_and_analysis_methods units String unitless
variable instrument_and_model String
attribute instrument_and_model bcodmo_name String instrument
attribute instrument_and_model description String Name of sequencing instruments
attribute instrument_and_model long_name String Instrument And Model
attribute instrument_and_model units String unitless
variable Analysis_methods String
attribute Analysis_methods bcodmo_name String sampling_method
attribute Analysis_methods description String Description of analysis methods
attribute Analysis_methods long_name String Analysis Methods
attribute Analysis_methods units String unitless

 
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