URLhttps://www.bco-dmo.org/dataset/709543
Download URLhttps://www.bco-dmo.org/dataset/709543/data/download
Media Typetext/tab-separated-values
CreatedJuly 24, 2017
ModifiedMarch 26, 2019
StateFinal no updates expected
Brief DescriptionOxygen consumption rates/zero valent iron dissolution of FeOB with kanamycin addition - Ferrozine assay

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 30 mg zero valent iron 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 3 days of incubation, the concentration of Fe(II) in the media was measured by ferrozine assay. Old media was then removed and replaced with fresh media containing 30 ng/ml kanamycin to prevent growth of remaining cells. The headspace was again filled with the same gas mix and oxygen concentrations were measured in real-time in each vial. Fe(II) concentration was determined daily by ferrozine assay for 3 more days.

Processing Description

Data was acquired using PreSens Measurement Studio 2 RC4 v0.5.6039.20506

Oxygen concentration readings cut out for PV-1 after approximately 4 days - will be fixed in future experiment.

BCO-DMO Data Processing Notes:
-Reformatted column names to comply with BCO-DMO standards
-Reformatted dates from mm/dd/yy to yyyy/mm/dd
-Replaced spaces with underscores
-Replaced N/A with nd

Instruments

Cary 100 UV-Vis Spectrophotometer (Agilent Technologies) [Spectrophotometer]
Details
Instance Description (Cary 100 UV-Vis Spectrophotometer (Agilent Technologies))

Used to measure ferrozine assay

An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.

PreSens OXY-4 SMA four channel optode and PreSens Pst3 optode sensor spots [Optode]
Details
Instance Description (PreSens OXY-4 SMA four channel optode and PreSens Pst3 optode sensor spots)

Used with air saturated water and 100% nitrogen gas.

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

Parameters

vial [sample]
Details
vial
[strain] ASWkan ferrozine sample description

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

date [date]
Details
date
Date measurement was taken; 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)

treatment [treatment]
Details
treatment
Whether measurement was of starting media (ASW) or replacement media (ASW + Kan)

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.

time_elapsed [time_elapsed]
Details
time_elapsed
Time since start of experiment
Elapsed time. Typically found in CTD profile data. Units can be seconds, minutes, etc.
Fe_II_concentration [Fe]
Details
Fe_II_concentration
Concentration of Fe(II) in media (average of triplicate samples)
Fe (Iron) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
standard_deviation [standard deviation]
Details
standard_deviation
Standard deviation of triplicate samples
Generic standard deviation value, taking on the units of the parameter that it is tied to.

Dataset Maintainers

NameAffiliationContact
Peter R. GirguisHarvard University
David EmersonBigelow Laboratory for Ocean Sciences
Jacob CohenHarvard University
Hannah AkeWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleCollaborative Research: The Role of Iron-oxidizing Bacteria in the Sedimentary Iron Cycle: Ecological, Physiological and Biogeochemical Implications
AcronymSedimentaryIronCycle
URLhttps://www.bco-dmo.org/project/544584
CreatedJanuary 8, 2015
ModifiedJune 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.

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