ERDDAP > info > bcodmo_dataset_737962

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	[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)		F   I   M	background			BCO-DMO	bcodmo_dataset_737962

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,.esriCsv,.geoJson
attribute	NC_GLOBAL	acquisition_description	String	Sediment cores were retrieved from bioturbated, intertidal sediments at low tide with a 7.5 cm (inner diameter) clear Plexiglas liner by pushing it directly into the sediment with minimum pressure as not to artificially force the sediment horizons together. The end of the core (i.e., the deepest horizon) was plugged with a rubber stopper and the sediment core was placed on ice. Typical transport back to the laboratory for pore water extraction was 0.5 hours. Sediment temperature and bottom water salinity were recorded at the time of sampling with an alcohol thermometer and refractometer, respectively. Once back to the laboratory, the cores were removed from ice and 5 cm Rhizons (0.16-0.19 um pore size) were inserted into pre-drilled 7 mm holes at 1 cm depth intervals to a depth of 10 cm. Pore waters were extracted by pulling negative pressure on the Rhizon with a 10 mL sterile syringe and holding the syringe plunger in place with a small wooden block placed between the syringe body and the plunger. Once pore water was extracted in the syringe, it was removed from the Rhizon, dispensed into a 15 mL centrifuge tube, and 250 uL of pore water was immediately transferred to 250 uL of Ferrozine buffer (10 mM in 50 mM HEPES buffer) and read on a MultiSkan MCC plate reader at 562 nm absorbance. The sediment core was then extruded and sliced into 1 cm intervals and dried in an oven at 70-80 degrees C for 24 hours, and then poorly- crystalline iron oxides (i.e., ferrihydrite and lepidocrocite) were extracted with 1 M hydroxylamine HCl in 25 % acetic acid (v/v) for 48 hours on a rotating shaker at 200 rpm. The extractions were allowed to settle for a few hours, then 10 uL was diluted into 990 uL (1:100 dilution) of distilled water containing 100 uL of Ferrozine buffer. The samples were read as above at 562 nm on the Multiskan MCC plate reader. Note: 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
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 PI: David Emerson (Bigelow Laboratory for Ocean Sciences) Co-PI: Peter Girguis (Harvard University) Contact: Jacob Beam (Bigelow Laboratory for Ocean Sciences) 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/
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
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. In 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. Description 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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/737962
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
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. 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	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/
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/
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/
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/
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/
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)

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.