ERDDAP > info > bcodmo_dataset_732864

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data	graph		files	public	[57Fe Wall Loss Experiment] - 57Fe Wall Loss Experiment data collected as part of a method development study investigating the precipitation and wall loss of labeled 57Fe when added to M9 Minimal Media (EAGER: Iron-Virus Interactions in the Ocean)		I   M	background			BCO-DMO	bcodmo_dataset_732864

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	Refer to Supplemental File, \"57Fe Wall Loss Experiment diagram\" for the steps indicated in bold. All materials were soaked overnight with heating in 1.5% Citrad Citric Acid liquid cleaner in deionized water, rinsed in RO water, and soaked in 10% HCl in Milli-Q ultrapure water for one week (due to time constraints), then rinsed with MilliQ ultrapure water, let dry in an AirClean 400 work station overnight, and double-bagged in polyethylene bags (Mellett et al., 2017). M9 Minimal Media for bacterial cultures was made using Milli-Q ultrapure water, containing final concentrations of 33.7 mM Na\u2082HPO\u2084\u00b72H\u2082O, 22 mM KH\u2082PO\u2084, 8.56 mM NaCl, 18.7 mM NH\u2084Cl, 0.1 M magnesium chloride, 0.1 M calcium chloride, 2 mg/ml Thiamine HCl in 70% EtOH, and 20% Glucose (Kutter & Sulakvelidze, 2004). Half of the media was chelexed using Chelex-100 resin (Pai et al., 1988) that was not acid-cleaned (C), and half remained un-chelexed (B). Half of each treatment was spiked with 10 \u00b5M labeled \u2075\u2077FeSO\u2084(2) while half remained un-spiked (1). A volume of 25 ml was then filtered through either a 0.2 \u00b5m Sterivex PVDF syringe filter for the dissolved fraction (D), or a 0.02 \u00b5m Whatman Anatop syringe filter for the soluble fraction (S) (Gledhill & Buck, 2012). Samples were directly filtered into trace metal clean polycarbonate Erlenmeyer flasks, placed in a clean bag with a small opening to vent, and left shaking at 37 \u00b0C for one week. Samples of each treatment were taken initially, then after the 1st, 3rd, and 7th days (t= 00, 01, 03, 07). The samples were diluted, acidified, and analyzed using an ELEMENT XR High Resolution Inductively Coupled Plasma Mass Spectrometer (HR-ICP-MS). The limit of detection (LOD) for \u2075\u2076Fe and \u2075\u2077Fe were 0.3 nM and 0.012 nM, respectively (Shrivastava & Gupta, 2011). Problem Report: \u200bThe original measurements of the M9 minimal media \u2075\u2076Fe contamination was high, so in an attempt to lower background contamination the media was chelexed. However, the Chelex-100 resin was not rinsed with acid, so was less active for removal of metals. This resulted in higher than expected background concentrations of metals. Three samples were contaminated with bacterial growth (as indicated by visual turbidity and confirmed using SYBR nucleic acid stain and epifluorescence microscopy) over the course of the week. On t=3, sample B2 was contaminated. By t=7, sample B1D and B1S were contaminated.
attribute	NC_GLOBAL	awards_0_award_nid	String	713366
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1722761
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1722761
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	Michael E. Sieracki
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50446
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	57Fe Wall Loss Experiment PIs: Kristen Buck & Mya Breitbart (USF) Co-PIs: Salvatore Caprara & Chelsea Bonnain (USF) Verion: 04 April 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/
attribute	NC_GLOBAL	data_source	String	extract_data_as_tsv version 2.3 19 Dec 2019
attribute	NC_GLOBAL	date_created	String	2018-04-04T17:40:41Z
attribute	NC_GLOBAL	date_modified	String	2020-02-11T18:33:18Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.732864.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/732864
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	ICP Mass Spec
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	ELEMENT XR High Resolution Inductively Coupled Plasma Mass Spectrometer (HR-ICP-MS)
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	732867
attribute	NC_GLOBAL	instruments_0_description	String	An ICP Mass Spec is an instrument that passes nebulized samples into an inductively-coupled gas plasma (8-10000 K) where they are atomized and ionized. Ions of specific mass-to-charge ratios are quantified in a quadrupole mass spectrometer.
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB15/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Inductively Coupled Plasma Mass Spectrometer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	530
attribute	NC_GLOBAL	instruments_0_supplied_name	String	ELEMENT XR High Resolution Inductively Coupled Plasma Mass Spectrometer
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chelex, chemical, data, dataset, date, day, description, dmo, erddap, fe56, fe57, Fe57_SPIKE, Fe57_to_Fe56, filter, FILTER_SIZE, management, notes, oceanography, office, preliminary, sample, SAMPLE_ID, size, spike
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/732864/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/732864
attribute	NC_GLOBAL	param_mapping	String	{'732864': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/732864/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of South Florida
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	USF
attribute	NC_GLOBAL	people_0_person_name	String	Mya Breitbart
attribute	NC_GLOBAL	people_0_person_nid	String	51740
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	University of South Florida
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	USF
attribute	NC_GLOBAL	people_1_person_name	String	Kristen N. Buck
attribute	NC_GLOBAL	people_1_person_nid	String	51624
attribute	NC_GLOBAL	people_1_role	String	Principal Investigator
attribute	NC_GLOBAL	people_1_role_type	String	originator
attribute	NC_GLOBAL	people_2_affiliation	String	University of South Florida
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	USF
attribute	NC_GLOBAL	people_2_person_name	String	Chelsea Bonnain
attribute	NC_GLOBAL	people_2_person_nid	String	732872
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	University of South Florida
attribute	NC_GLOBAL	people_3_affiliation_acronym	String	USF
attribute	NC_GLOBAL	people_3_person_name	String	Salvatore Caprara
attribute	NC_GLOBAL	people_3_person_nid	String	732874
attribute	NC_GLOBAL	people_3_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_3_role_type	String	originator
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	Shannon Rauch
attribute	NC_GLOBAL	people_4_person_nid	String	51498
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	Fe-Virus
attribute	NC_GLOBAL	projects_0_acronym	String	Fe-Virus
attribute	NC_GLOBAL	projects_0_description	String	Iron is an essential micronutrient for phytoplankton that is required for photosynthesis and respiration. Insufficient iron has been shown to limit phytoplankton growth in large regions of the surface ocean, and correspondingly, iron cycling is directly linked to carbon cycling in much of the marine environment. Nearly all iron in seawater (>99%) exists as complexes with organic molecules called ligands, which govern the concentration of iron dissolved in the water and the bioavailability of that iron to phytoplankton. However, despite the importance of iron-binding organic ligands, their sources and identities are largely unknown. Viruses, the majority of which are phages (viruses that infect bacteria), are extremely abundant in seawater and are in the same size fraction as dissolved iron. Recent evidence that non-marine phages contain iron as part of their structures has led to the proposal that marine phages may represent a previously overlooked class of organic iron-binding ligands. This project is determining the contribution of marine phages to dissolved iron pools and culture phage-host systems in the laboratory to determine if phages utilize bacterial iron-uptake receptors for infection in the manner of a Trojan horse. As the first study to examine the biogeochemical impact of trace elements contained within the structure of highly abundant marine phage particles, successful completion of the proposed research will be transformative for biological and chemical oceanography and have far-reaching implications for other fields, including human health where iron availability plays an important role in microbial pathogenesis. This project contributes to the multidisciplinary training of a graduate student and postdoctoral researcher. Research results will be disseminated through scientific publications and presentations, and the public will be educated about linkages between viruses and ocean chemistry via a hands-on exhibit for the annual St. Petersburg Science Festival. Building upon evidence from non-marine model systems demonstrating the presence of iron ions in phage tail proteins and phage utilization of cell surface receptors for siderophore-bound iron, this project combines field and laboratory-based experiments to test the following three hypotheses regarding iron-virus interactions in the oceans: (1) Iron incorporated into phage tails originates from bacterial cell reserves, reducing the amount of iron available for remineralization upon lysis; (2) Phages constitute important iron-binding ligands in the oceans, accounting for a substantial portion of organically complexed colloidal dissolved iron; (3) Marine phages compete with siderophore-bound iron for uptake receptors on the bacterial cell surface and use iron in their tails as a Trojan horse for infection. Initial calculations predict that phages could account for up to 70% of the colloidal fraction of organically complexed dissolved iron in the surface ocean; therefore, this project is critical for advancing knowledge of trace-metal cycling as well as phage-host interactions. Additionally, if a portion of the cellular iron thought to be released from bacterial cells for remineralization following lysis is already incorporated into phage tails, then these findings will have significant implications for oceanic biogeochemical models. Through a combination of laboratory-based culture experiments and field sample measurements, this project could reveal the identity of a ubiquitous component of colloidal organic iron-binding ligands, modify the estimates of iron concentrations and species released through viral lysis, and potentially identify a novel receptor type for marine phage that may compete with the acquisition of siderophore-bound iron by host bacteria.
attribute	NC_GLOBAL	projects_0_end_date	String	2019-01
attribute	NC_GLOBAL	projects_0_name	String	EAGER: Iron-Virus Interactions in the Ocean
attribute	NC_GLOBAL	projects_0_project_nid	String	713367
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	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	DATE
attribute	NC_GLOBAL	summary	String	This data was collected as part of a method development study investigating the precipitation and wall loss of labeled \u2075\u2077Fe when added to M9 Minimal Media, which is used to grow the model bacterial species Escherichia coli. The bulk media was prepared with the same components and a portion was treated with Chelex-100 to remove metals, while the other portion remained un-chelexed. Half of each treatment was spiked with labeled \u2075\u2077Fe and either 0.2 \u03bcm or 0.02 \u03bcm filtered for comparison of the dissolved and soluble fractions. The \u2075\u2077Fe content was monitored over four time points for one week in a shaking incubator, under the same conditions used to culture E. coli for labeling experiments.
attribute	NC_GLOBAL	title	String	[57Fe Wall Loss Experiment] - 57Fe Wall Loss Experiment data collected as part of a method development study investigating the precipitation and wall loss of labeled 57Fe when added to M9 Minimal Media (EAGER: Iron-Virus Interactions in the Ocean)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	DATE		int
attribute	DATE	_FillValue	int	2147483647
attribute	DATE	actual_range	int	20171113, 20171113
attribute	DATE	bcodmo_name	String	date
attribute	DATE	description	String	Date (UTC) when media was filtered and experiment initiated (t=0), in format YYYYMMDD
attribute	DATE	long_name	String	DATE
attribute	DATE	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/
attribute	DATE	units	String	unitless
variable	SAMPLE_ID		String
attribute	SAMPLE_ID	bcodmo_name	String	sample
attribute	SAMPLE_ID	description	String	Sample identifier designated B for un-chelexed, or C for chelexed; 1 for un-spiked with 57FeSO4, 2 for spiked with 10 uM 57FeSO4; D for dissolved (0.2 um filtered) or S for soluble (0.02 um filtered)
attribute	SAMPLE_ID	long_name	String	SAMPLE ID
attribute	SAMPLE_ID	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	SAMPLE_ID	units	String	unitless
variable	DESCRIPTION		String
attribute	DESCRIPTION	bcodmo_name	String	treatment
attribute	DESCRIPTION	description	String	Description of treatment type
attribute	DESCRIPTION	long_name	String	DESCRIPTION
attribute	DESCRIPTION	units	String	unitless
variable	CHELEX		String
attribute	CHELEX	bcodmo_name	String	treatment
attribute	CHELEX	description	String	Solution was treated with Chelex-100 resin (Yes) or not (No), units in Yes/No
attribute	CHELEX	long_name	String	CHELEX
attribute	CHELEX	units	String	unitless
variable	Fe57_SPIKE		byte
attribute	Fe57_SPIKE	_FillValue	byte	127
attribute	Fe57_SPIKE	actual_range	byte	0, 10
attribute	Fe57_SPIKE	bcodmo_name	String	treatment
attribute	Fe57_SPIKE	description	String	57FeSO4 spike concentration as added to the media
attribute	Fe57_SPIKE	long_name	String	Fe57 SPIKE
attribute	Fe57_SPIKE	units	String	micromolar (uM)
variable	FILTER_SIZE		String
attribute	FILTER_SIZE	bcodmo_name	String	filter_size
attribute	FILTER_SIZE	description	String	Pore size used to filter media, using 0.2 um Sterivex PVDF syringe filter or 0.02 um Anatop syringe filter
attribute	FILTER_SIZE	long_name	String	FILTER SIZE
attribute	FILTER_SIZE	units	String	micrometers (um)
variable	DAY		byte
attribute	DAY	_FillValue	byte	127
attribute	DAY	actual_range	byte	0, 7
attribute	DAY	bcodmo_name	String	days
attribute	DAY	description	String	Time when treatment was sampled, t=n, units in days
attribute	DAY	long_name	String	DAY
attribute	DAY	units	String	days
variable	Fe56		float
attribute	Fe56	_FillValue	float	NaN
attribute	Fe56	actual_range	float	10.73, 738.92
attribute	Fe56	bcodmo_name	String	Fe
attribute	Fe56	description	String	Concentration of 56Fe as determined by HR-ICP-MS
attribute	Fe56	long_name	String	Fe56
attribute	Fe56	units	String	nanomolar (nM)
variable	Fe57		float
attribute	Fe57	_FillValue	float	NaN
attribute	Fe57	actual_range	float	2.13, 10857.82
attribute	Fe57	bcodmo_name	String	Fe
attribute	Fe57	description	String	Concentration of 57Fe as determined by HR-ICP-MS
attribute	Fe57	long_name	String	Fe57
attribute	Fe57	units	String	nanomolar (nM)
variable	Fe57_to_Fe56		float
attribute	Fe57_to_Fe56	_FillValue	float	NaN
attribute	Fe57_to_Fe56	actual_range	float	2.27, 2459.01
attribute	Fe57_to_Fe56	bcodmo_name	String	Fe
attribute	Fe57_to_Fe56	description	String	Ratio of 57Fe concentration to 56Fe concentration as measured by the HR-ICP-MS, multiplied by 100 (in percentage)
attribute	Fe57_to_Fe56	long_name	String	Fe57 To Fe56
attribute	Fe57_to_Fe56	units	String	unitless (percentage)
variable	NOTES		String
attribute	NOTES	bcodmo_name	String	comment
attribute	NOTES	description	String	Some samples contaminated by bacterial growth were designated as such
attribute	NOTES	long_name	String	NOTES
attribute	NOTES	units	String	unitless

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.