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Title Sum-
Institution Dataset ID
     data   graph     files  public Oxygen consumption rates/zero valent iron dissolution of FeOB with kanamycin addition -
replacement samples
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The Dataset's Variables and Attributes

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 These data were collected by placing each strain in a 100 mL serum vial with 6
mL of their standard, published media with 30 mg zero valent iron as a source
of Fe(II).\u00a0 The headspace was filled with a gas mix of 8% oxygen/10%
carbon dioxide/82% nitrogen by using bottled gas mixes and a regulator to
flush the headspace without over pressurization.\u00a0 Prior to sealing the
serum vials, a\u00a0Presens\u00a0OPTODE dot (sensor) was placed inside the
vial, allowing non-invasive gas sampling of the changes in O2 in the
headspace.\u00a0 A\u00a0Presens\u00a0four channel system was used to measure
changes in oxygen concentration in real-time in each bottle.\u00a0 A total of
four channels were measured during each experiment: channels 1 through 3 are
the biological treatments and channel 4 was a\u00a0kill\u00a0control (microbes
were by placing on a heat block at 100 degrees C for 5 minutes). After 3 days
of incubation, the concentration of Fe(II) in the media was measured by
ferrozine assay. Old media was then removed and replaced with fresh media
containing 30 ng/ml kanamycin to prevent\u00a0growth\u00a0of remaining cells.
The headspace was again filled with the same gas mix and oxygen concentrations
were measured in real-time in each vial. Fe(II) concentration was determined
daily by ferrozine assay for 3 more days.
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 Replacement Vial Data
P. Girguis and D. Emerson, PIs
Version 21 July 2017
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 2017-07-24T19:25:27Z
attribute NC_GLOBAL date_modified String 2019-03-26T17:06:07Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.709573.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/709573 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Used with air saturated water and 100% nitrogen gas.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 709581
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 OXY-4 SMA four channel optode and PreSens Pst3 optode sensor spots
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, chemical, concentration, data, dataset, date, dmo, elapsed, erddap, iso, management, O2, oceanography, office, oxygen, oxygen_concentration, preliminary, time, time2, time_elapsed, treatment, vial
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/709573/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/709573 (external link)
attribute NC_GLOBAL param_mapping String {'709573': {'ISO_DateTime_UTC': 'flag - time'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/709573/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 Jacob Cohen
attribute NC_GLOBAL people_2_person_nid String 650331
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 Hannah Ake
attribute NC_GLOBAL people_3_person_nid String 650173
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.
Intellectual 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.
Broader 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 summary String Oxygen consumption rates/zero valent iron dissolution of FeOB with kanamycin addition - replacement samples
attribute NC_GLOBAL time_coverage_end String 2016-11-17T04:49:53Z
attribute NC_GLOBAL time_coverage_start String 2016-11-02T07:03:26Z
attribute NC_GLOBAL title String Oxygen consumption rates/zero valent iron dissolution of FeOB with kanamycin addition - replacement samples
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable vial   String  
attribute vial bcodmo_name String sample
attribute vial description String [strain] ASWkan replacement sample description
attribute vial long_name String Vial
attribute vial nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute vial units String unitless
variable date   String  
attribute date bcodmo_name String date
attribute date description String Date measurement was taken; YYYY/MM/DD
attribute date long_name String Date
attribute date nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute date time_precision String 1970-01-01
attribute date units String unitless
variable time2   String  
attribute time2 bcodmo_name String time
attribute time2 description String Time measurement was taken; HH:MM:SS
attribute time2 long_name String Time
attribute time2 nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/ (external link)
attribute time2 units String unitless
variable treatment   String  
attribute treatment bcodmo_name String treatment
attribute treatment description String Number of vial measured or control
attribute treatment long_name String Treatment
attribute treatment units String unitless
variable time_elapsed   float  
attribute time_elapsed _FillValue float NaN
attribute time_elapsed actual_range float 0.0, 8492.886
attribute time_elapsed bcodmo_name String time_elapsed
attribute time_elapsed description String Time since start of experiment
attribute time_elapsed long_name String Time Elapsed
attribute time_elapsed nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/ (external link)
attribute time_elapsed units String minutes
variable oxygen_concentration   float  
attribute oxygen_concentration _FillValue float NaN
attribute oxygen_concentration actual_range float 76.96, 110.5
attribute oxygen_concentration bcodmo_name String O2_umol_L
attribute oxygen_concentration description String Concentration of oxygen inside vial
attribute oxygen_concentration long_name String Oxygen Concentration
attribute oxygen_concentration units String umol/L
variable time   double  
attribute time _CoordinateAxisType String Time
attribute time actual_range double 1.478070206E9, 1.479358193E9
attribute time axis String T
attribute time bcodmo_name String ISO_DateTime_UTC
attribute time description String Date and time (UTC) formatted to ISO8601 standard. T indicates start of time string; Z indicates UTC.
attribute time ioos_category String Time
attribute time long_name String ISO Date Time UTC
attribute time nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/ (external link)
attribute time source_name String ISO_DateTime_UTC
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

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

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