Download URLhttps://www.bco-dmo.org/dataset/650324/data/download
Media Type text/tab-separated-values
Created June 29, 2016
Modified June 6, 2019
State Final no updates expected
Brief Description

O2 consumption of two strains of Mariprofundus ferrooxydans at two O2 conc.

Acquisition Description

The cultivars of the neutrophilic iron oxidizers Mariprofundus ferrooxydans PV-1 and “TAG-1” were obtained from the Emerson lab at Bigelow laboratories.

Processing Description

These data were collected by placing each strain in a 100 mL serum vial with 6 mL of their standard, published media.  The headspace was filled with the appropriate oxygen concentration by using bottled gas mixes and a regulator to flush the headspace without overpressurization.  Prior to sealing the serum vials, a Presens OPTODE dot (sensor) was placed inside the vial, allowing non-invasive gas sampling of the changes in O2 in the headspace.  A Presens four channel system was used to measure changes in oxygen concentration in realtime in each bottle.  A total of four channels were measured during each experiment: channels 1 through 3 are the biological treatments and channel 4 was a kill control (microbe were killed through 24 hours of exposure to gamma radiation).

DMO notes:
Made top level .dat file from two elements in the filename: strain and O2 concentration
Removed units from data set, including umols/L and degrees C
changed treatment 4 to kill
changed from channel to treatment for column name
normalized variable names to BCO-DMO standards


PreSens OPTODE dot [Optode]
Instance Description (PreSens OPTODE dot)

A Presens™ OPTODE dot (sensor) was placed inside the sample vial, allowing non-invasive gas sampling of the changes in O2 in the headspace.

For more information about the PreSens OPTODE sensor, read this.

An optode or optrode is an optical sensor device that optically measures a specific substance usually with the aid of a chemical transducer.


FeOB_strain [brief_desc]
strain of iron oxidizing bacteria (PV-1 or TAG-1)

brief description, open ended, specific to the data set in which it appears

temp [temperature]
the temperature at which the experiments were conducted; the whole experiment was conducted at 20 degrees
water temperature at measurement depth
O2_conc [O2_umol_L]
the oxygen concentration to which the bacteria were exposed

Oxygen; dissolved; reported in units of micromoles/liter

treatment [treatment]
original name: channel; channels 1 through 3 are the biological treatments and channel 4 was a kill control

Experimental conditions applied to experimental units.  In comparative experiments, members of the complementary group, the control group, receive either no treatment or a standard treatment.

date_local [date_local]
the range of dates the experiment took place

local month, day and year, usually as a text string, e.g. feb10_1995. It is better to use one of the other forms of presenting date and time data so that the data can be used in computations and for comparisons. Note, if the string begins with numbers but also includes letters, there may be problems using the field name for retrieval.

time_local [time_local]
time at which measurements were recorded (hour:minutes)

time of day, local time, using 2400 clock format

O2_consume [O2_umol_L]
oxygen consumption

Oxygen; dissolved; reported in units of micromoles/liter

yrday_local [yrday_local]
day of the year including decimals; added by DMO
local day and decimal time, as 326.5 for the 326th day of the year, or November 22 at 1200 hours (noon)
ISO_DateTime_Local [ISO_DateTime_Local]

date and time formatted to ISO 8601 standard; added by DMO. in the format YYYY-mm-ddTHH:MM:SS.xx.

Date/Time (Local) ISO formatted
This standard is based on ISO 8601:2004(E) and takes on any of the following forms:
2009-08-30T09:05:00[.xx] (local time)
2009-08-30T14:05:00[.xx]Z (UTC time)
The dashes and the colons can be dropped.
The T can also be dropped "by mutual agreement", but one needs the trailing Z if the time is UTC.

Note the Time Zone (TZ) as +/-HH:MM
Time Zone signage is for conversion from local to UTC
West Coast USA in summer is +7 (add 7 hrs to local time for UTC)

Dataset Maintainers

Peter R. GirguisHarvard University
David EmersonHarvard University
David JohnstonBigelow Laboratory for Ocean Sciences
Jacob CohenBigelow Laboratory for Ocean Sciences
Hannah AkeHarvard University
Hannah AkeHarvard University
Hannah AkeWoods 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