Created June 28, 2019
Modified July 1, 2019
State Final no updates expected
Brief Description

Experimental oxygen consumption data for two iron oxidizing bacteria with pyrrhotite as iron source..

Acquisition Description

These data were collected by placing each strain in a 100 mL serum vial with 6 mL of their standard, published media with 200 mg pyrrhotite powder as a source of Fe(II).  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.  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 real-time 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 (microbes were by placing on a heat block at 100 degrees C for 5 minutes). After 14 days of incubation at 20˚C, vial headspace were replaced with the original starting gas mix. Incubation then continued for 7 more days.

Processing Description

BCO-DMO Data Processing Notes:
– Concatenated sheets PV-1 pyrrhotite and TAG-1 pyrrhotite together
– Created column for ‘bact’ which contains the sheet name.
– Removed last two rows of data file as they were repeats of the header.
– Combined “Date” and “Time” columns into “ISO_DateTime” column.


PreSens OXY-4 SMA 4-channel optode [Dissolved Oxygen Sensor]
Instance Description (PreSens OXY-4 SMA 4-channel optode)

A PreSens OXY-4 SMA 4-channel optode was used for oxygen concentration measurements.

An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed


Date [date]
Date of measurement (yyyy-mm-dd)

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)

Time [time]
Time of measurement (HH:MM:SS)
Time GMT defined as HHMM; time of day; generally reported in GMT as HHMM (hours and minutes) but may also be HH.H (decimal hours) or HHMMSS (hours; minutes and seconds); in EqPac time is reported as Hawaii local time
Channel [sample_descrip]
Number of test vial (1-3 = live cells; 4 = killed control)
text description of sample collected
delta_t [duration]
time since experiment start

Duration of treatment, observation or sampling

Oxygen concentration

dissolved oxygen concentration

iron oxidizing bacteria
text description of sample collected
ISO_DateTime [unknown]

Date and time, Eastern, in ISO 8601 format (yyyy-mm-ddTHH:MM:SS)

association with a community-wide standard parameter is not yet defined

Dataset Maintainers

Peter R. GirguisHarvard University
David EmersonHarvard University
Jacob CohenBigelow Laboratory for Ocean Sciences
Mathew BiddleBigelow Laboratory for Ocean Sciences
Mathew BiddleWoods 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