Dataset: Oxygen Consumption Rates of Iron Oxidizing Bacteria - FeOB

Name: Laboratory experiment data describing oxygen consumption of two strains of Mariprofundus ferrooxydans at two oxygen concentrations and one temperature (Sedimentary Iron Cycle project)
Published: 2016-06-29
License: https://creativecommons.org/licenses/by/4.0/
Keywords: biota, oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.650324.1

Temporal Extent: 2016-03-16 - 2016-05-23

Project:

Collaborative Research: The Role of Iron-oxidizing Bacteria in the Sedimentary Iron Cycle: Ecological, Physiological and Biogeochemical Implications (SedimentaryIronCycle)

Principal Investigator:

Peter Girguis (Harvard University)

Co-Principal Investigator:

David Emerson (Bigelow Laboratory for Ocean Sciences)

David Johnston (Harvard University)

Contact:

Jacob Cohen (Harvard University)

BCO-DMO Data Manager:

Hannah Ake (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2016-06-29

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Data URL:

https://www.bco-dmo.org/dataset/650324/data

Laboratory experiment data describing oxygen consumption of two strains of Mariprofundus ferrooxydans at two oxygen concentrations and one temperature (Sedimentary Iron Cycle project)

Abstract:

Laboratory experiment data describing oxygen consumption of two strains of Mariprofundus ferrooxydans at two oxygen concentrations and one temperature (Sedimentary Iron Cycle project)

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2016-06-29	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.650324.1	2019-06-06

Description

In these experiments, oxygen consumption rates were measured for the iron-oxidizing bacteria (FeOB) Mariprofundus ferrooxydans PV-1 as well as the neutrophilic FeOB "TAG-1" (An isolate from hydrothermal vents in the Mid Atlantic ridge that has not yet been formally named. TAG simply refers to the TAG hydrothermal site from which this microbe was isolated.). These experiments have examined oxygen consumption at two oxygen concentrations (100 uM and 25 uM) at one temperature (20 degrees C).

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

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1459252

Deployments

None available yet

Instruments

Optode

(more info)

Short Name:

Generic Description

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

PI supplied instrument name: PreSens OPTODE dot

Dataset-specific description

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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
FeOB_strain	strain of iron oxidizing bacteria (PV-1 or TAG-1)	unitless	brief_desc
temp	the temperature at which the experiments were conducted; the whole experiment was conducted at 20 degrees	degrees celsius	temp
O2_conc	the oxygen concentration to which the bacteria were exposed	micromoles per liter	O2_umol_L
treatment	original name: channel; channels 1 through 3 are the biological treatments and channel 4 was a kill control	unitless	treatment
date_local	the range of dates the experiment took place	unitless	date_local
time_local	time at which measurements were recorded (hour:minutes)	unitless	time_local
O2_consume	oxygen consumption	micromoles per liter	O2_umol_L
yrday_local	day of the year including decimals; added by DMO	decimal day	yrday_local
ISO_DateTime_Local	date and time formatted to ISO 8601 standard; added by DMO. in the format YYYY-mm-ddTHH:MM:SS.xx.	unitless	ISO_DateTime_Local