Download URLhttps://www.bco-dmo.org/dataset/737962/data/download
Media Type text/tab-separated-values
Created June 1, 2018
Modified March 15, 2019
State Final no updates expected
Brief Description

Pore water and solid phase iron geochemical data

Acquisition Description

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 .

Processing Description

BCO-DMO Processing:
– separated lat and long into different columns;
– modified parameter names to conform with BCO-DMO naming conventions;
– changed date format to yyyymmdd.



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/

Handheld salinity refractometer with temperature compensation (Marine Depot) [Refractometer]

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.

MultiSkan MCC plate reader [plate reader]

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: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.


site [site]

Name of sampling site

Sampling site identification.
lat [latitude]

Latitude of sampling site

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

long [longitude]

Longitude of sampling site

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

date [date]

Date of sampling; formatted as yyyymmdd

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

depth [depth]

Sampling depth

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

When used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

sed_temp [temperature]
Sediment temperature

Temperature in degrees C of a sample or other item.  A generic temperature measurement.

Note: This is NOT water temp or sea surface temp

salinity [sal]
Low tide surface water salinity

salinity, calculated from the CTD 'primary sensors' of conductivity and temperature, Practical Salinity Scale (PSS-78), dimensionless. Depending on the input source, salinity from the primary sensors can have a variety of names i.e. s0, s00, sal0, sal00.

ferrous_iron [Fe]
Dissolved pore water ferrous iron

Iron (Fe). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.

poorly_crystalline_iron_oxide [Fe]
Sedimentary poorly-crystalline iron oxide Fe

Iron (Fe). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.

Dataset Maintainers

David EmersonBigelow Laboratory for Ocean Sciences
Peter R. GirguisBigelow Laboratory for Ocean Sciences
Jacob BeamHarvard University
Shannon RauchHarvard University
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Collaborative Research: The Role of Iron-oxidizing Bacteria in the Sedimentary Iron Cycle: Ecological, Physiological and Biogeochemical Implications
Acronym SedimentaryIronCycle
Created January 8, 2015
Modified June 1, 2018
Project Description

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.

Data Project Maintainers
David EmersonBigelow Laboratory for Ocean SciencesPrincipal Investigator
Peter R. GirguisHarvard UniversityPrincipal Investigator
David JohnsonHarvard UniversityCo-Principal Investigator