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
attribute NC_GLOBAL acquisition_description String The cultivars of the neutrophilic iron oxidizers Mariprofundus ferrooxydans\nPV-1 and \\\"TAG-1\\\" were obtained from the Emerson lab at Bigelow laboratories.
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 O2 consumption; Iron Oxidizing bacteria \n  MultiChannelStudio Version 1.0.16.0 \n   P. Girguis and D. Emerson, PIs \n  version 29 June 2016
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 2016-06-29T19:59:40Z
attribute NC_GLOBAL date_modified String 2019-06-06T19:05:08Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.650324.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/650324 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_dataset_instrument_description String A Presens™ OPTODE dot (sensor) was placed inside the sample vial, allowing non-invasive gas sampling of the changes in O2 in the headspace.\nFor more information about the PreSens OPTODE sensor, read this.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 650372
attribute NC_GLOBAL instruments_0_description String An optode or optrode is an optical sensor device that optically measures a specific substance usually with the aid of a chemical transducer.
attribute NC_GLOBAL instruments_0_instrument_name String Optode
attribute NC_GLOBAL instruments_0_instrument_nid String 727
attribute NC_GLOBAL instruments_0_supplied_name String PreSens OPTODE dot
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, chemical, conc, consume, data, dataset, date, date_local, dmo, erddap, FeOB_strain, iso, local, management, O2, O2_conc, O2_consume, oceanography, office, oxygen, preliminary, strain, temperature, time, time_local, treatment, yrday, yrday_local
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/650324/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/650324 (external link)
attribute NC_GLOBAL param_mapping String {'650324': {'ISO_DateTime_Local': 'flag - time'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/650324/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 Bigelow Laboratory for Ocean Sciences
attribute NC_GLOBAL people_1_person_name String David Emerson
attribute NC_GLOBAL people_1_person_nid String 544585
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 Harvard University
attribute NC_GLOBAL people_2_person_name String David Johnston
attribute NC_GLOBAL people_2_person_nid String 650329
attribute NC_GLOBAL people_2_role String Co-Principal Investigator
attribute NC_GLOBAL people_2_role_type String originator
attribute NC_GLOBAL people_3_affiliation String Harvard University
attribute NC_GLOBAL people_3_person_name String Jacob Cohen
attribute NC_GLOBAL people_3_person_nid String 650331
attribute NC_GLOBAL people_3_role String Contact
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL people_4_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_4_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_4_person_name String Hannah Ake
attribute NC_GLOBAL people_4_person_nid String 650173
attribute NC_GLOBAL people_4_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_4_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 standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String temp
attribute NC_GLOBAL summary String Laboratory experiment data describing oxygen consumption of two strains of Mariprofundus ferrooxydans at two oxygen concentrations and one temperature (Sedimentary Iron Cycle project)
attribute NC_GLOBAL time_coverage_end String 2016-05-23T03:53:24Z
attribute NC_GLOBAL time_coverage_start String 2016-03-16T06:42:12Z
attribute NC_GLOBAL title String Laboratory experiment data describing oxygen consumption of two strains of Mariprofundus ferrooxydans at two oxygen concentrations and one temperature (Sedimentary Iron Cycle project)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable FeOB_strain String
attribute FeOB_strain bcodmo_name String brief_desc
attribute FeOB_strain description String strain of iron oxidizing bacteria (PV-1 or TAG-1)
attribute FeOB_strain long_name String Fe OB Strain
attribute FeOB_strain units String unitless
variable temp byte
attribute temp _FillValue byte 127
attribute temp actual_range byte 20, 20
attribute temp bcodmo_name String temperature
attribute temp description String the temperature at which the experiments were conducted; the whole experiment was conducted at 20 degrees
attribute temp long_name String Temperature
attribute temp nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/ (external link)
attribute temp units String degrees celsius
variable O2_conc byte
attribute O2_conc _FillValue byte 127
attribute O2_conc actual_range byte 25, 100
attribute O2_conc bcodmo_name String O2_umol_L
attribute O2_conc description String the oxygen concentration to which the bacteria were exposed
attribute O2_conc long_name String O2 Conc
attribute O2_conc units String micromoles per liter
variable treatment String
attribute treatment bcodmo_name String treatment
attribute treatment description String original name: channel; channels 1 through 3 are the biological treatments and channel 4 was a kill control
attribute treatment long_name String Treatment
attribute treatment units String unitless
variable date_local String
attribute date_local bcodmo_name String date_local
attribute date_local description String the range of dates the experiment took place
attribute date_local long_name String Date Local
attribute date_local time_precision String 1970-01-01
attribute date_local units String unitless
variable time_local String
attribute time_local bcodmo_name String time_local
attribute time_local description String time at which measurements were recorded (hour:minutes)
attribute time_local long_name String Time Local
attribute time_local units String unitless
variable O2_consume float
attribute O2_consume _FillValue float NaN
attribute O2_consume actual_range float 8.677, 104.391
attribute O2_consume bcodmo_name String O2_umol_L
attribute O2_consume description String oxygen consumption
attribute O2_consume long_name String O2 Consume
attribute O2_consume units String micromoles per liter
variable yrday_local double
attribute yrday_local _FillValue double NaN
attribute yrday_local actual_range double 75.27931, 143.16208
attribute yrday_local bcodmo_name String yrday_local
attribute yrday_local description String day of the year including decimals; added by DMO
attribute yrday_local long_name String Yrday Local
attribute yrday_local units String decimal day
variable time double
attribute time _CoordinateAxisType String Time
attribute time actual_range double 1.458110532E9, 1.463975604E9
attribute time axis String T
attribute time bcodmo_name String ISO_DateTime_Local
attribute time description String date and time formatted to ISO 8601 standard; added by DMO. in the format YYYY-mm-ddTHH:MM:SS.xx.
attribute time ioos_category String Time
attribute time long_name String ISO Date Time Local
attribute time source_name String ISO_DateTime_Local
attribute time standard_name String time
attribute time time_origin String 01-JAN-1970 00:00:00
attribute time time_precision String 1970-01-01T00:00:00Z
attribute time units String seconds since 1970-01-01T00:00:00Z

 
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