http://lod.bco-dmo.org/id/dataset/638091
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2016-02-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Effects of temperature on biomass and sulfide production in Desulfovibrio hydrothermals (INSPIRE_Pyrite project)
2016-02-09
publication
2016-02-09
revision
BCO-DMO Linked Data URI
2016-02-09
creation
http://lod.bco-dmo.org/id/dataset/638091
Peter Girguis
Harvard University
principalInvestigator
David Clarke
Harvard University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Girguis, P., Clarke, D. (2016) Effects of temperature on biomass and sulfide production in Desulfovibrio hydrothermals (INSPIRE_Pyrite project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version working) Version Date 2016-02-09 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/638091 [access date]
Effects of temp on biomass and sulfide production in Desulfovibrio hydrothermals AM13 Dataset Description: <p>Effects of temperature on biomass and sulfide production in <em>Desulfovibrio hydrothermalis strain AM13 </em>across a range of biologically relevant temperatures. Measured biomass production (cell concentration in stationary phase) and maximum sulfide concentration produced and maximum sulfide production rate in the exponential phase.</p>
<p>Figures included with the data:</p>
<p><img src="http://dmoserv3.bco-dmo.org/data_docs/INSPIRE_Pyrite/imageme.bmp" style="float:left" /><br />
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<p><img src="https://datadocs.bco-dmo.org/d3/data_docs/INSPIRE_Pyrite/sulfidecounts.bmp" style="float:left" /><br />
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<p>&nbsp;</p> Methods and Sampling: <p>Inoculum: 200 µl stock culture (stationary phase) into 50 ml medium (expected at t0: 8.0 E+5 cells/ml).</p>
<p>"The time between t0 and tend is variable.&nbsp; We wait to reach the stationary phase.&nbsp; The rate is the maximum rate (exponential phase of sulfide production)." A. Picard, personal communication.<br />
&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1344241 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1344241
onGoing
Peter Girguis
Harvard University
617-496-8328
Biological Laboratories, Room 3085 16 Divinity Ave
Cambridge
MA
02138-2020
USA
pgirguis@oeb.harvard.edu
pointOfContact
David Clarke
Harvard University
617-495-4140
School of Engineering and Applied Sciences 29 Oxford St., 303 Cruft Hall
Cambridge
MA
02138
clarke@seas.harvard.edu
pointOfContact
asNeeded
Dataset Version: working
Unknown
phase
temp
numb_cells_t0
numb_cells_tend
max_sulfide_prod
std_error_prod
max_sulfide_prod_rate
std_error_rate
Epifluorescence Microscope - Zeiss Axiophot
spectrophotometer
theme
None, User defined
brief description
water temperature at measurement depth
count
sulfide
standard error
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Fluorescence Microscope
Spectrophotometer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
INSPIRE Track 1: Microbial Sulfur Metabolism and its Potential for Transforming the Growth of Epitaxial Solar Cell Absorbers
https://osprey.bco-dmo.org/project/623700
INSPIRE Track 1: Microbial Sulfur Metabolism and its Potential for Transforming the Growth of Epitaxial Solar Cell Absorbers
<p>This INSPIRE award is partially funded by Biological Oceanography Program in Division of Ocean Sciences, in the Directorate of Geosciences; the Electronic and Photonic Materials Program in the Division of Materials Research, Directorate of Mathematical and Physical Sciences.</p>
<p>A simple idea motivates this project: By characterizing the mechanisms underlying pyrite film deposition by subsurface microbes living at hydrothermal vents, can approaches be developed to controllably grow high-purity pyrite films that could be used to produce low-cost photovoltaic solar cells? Recent in situ studies at hydrothermal vents have found "subsurface" microbes associated with the deposition of large crystalline metal sulfides (up to 1.1 millimeters), including iron pyrite. In laboratory incubations, vent microbes specifically deposited pyrite (FeS2), devoid of Zn, Cu and other metals that were abundant in the liquid media. Abiotic incubations did not exhibit this specificity. The investigators hypothesize that, in situ, microbes deposit pyrite via a number of potential processes, including a physiological process called extracellular electron transfer (EET), wherein microbes shuttle electrons to/from minerals. In situ, EET-enabled microbes may use conductive minerals to electrically access oxidants, and deposit pyrite on these surfaces. Vents are thus natural bioelectrochemical cells, which grow metal sulfides via microbial and abiotic electrochemical processes, though the details and mechanisms remain to be determined. This project is aimed at elucidating the mechanisms underlying microbial FeS2 pyrite bio-deposition, and assessing how microbes might be used to deposit epitaxial films for solar cells absorbers. FeS2 pyrite has been identified as prospective low cost solar absorbers because of their abundance, suitable band-gap (~0.95 eV) and high optical absorbance. Microbial pyrite film deposition at lower temperatures (<100 C) might offer a radically new, low cost approach to creating large area PV solar cells. Nothing is currently known about the mechanisms underlying microbial pyrite growth, though the large crystal sizes suggest epitaxial deposition is favored over re-nucleation implying that, once nucleated, epitaxial growth can occur. A series of experiments using natural vent microbial communities and isolates will be conducted to determine: A) environmental factors that influence bio-deposition; B) potential molecular mechanisms; C) the microstructural and electrical properties of these films; and D) whether bio-deposition by single species or consortia yields films of highest purity, size and homogeneity.</p>
<p>The project is both highly-integrated and transformative. It is relevant to our understanding of microbial sulfur cycling, as little is known about how microbes mediate crystalline pyrite formation and the degree to which this influences sulfur isotope geochemistry. Molecular studies will be used to interrogate relevant microbial metabolic processes and constrain the possible mechanisms of pyrite film growth, which is critical to advancing our ability to grow FeS2 films for device applications. Understanding the effects of substrate crystallography and electrical conductivity on the growth morphology will further inform our knowledge of microbial pyrite deposition. Notably, this research differ from existing biomimetic approaches. The studies are not focused on crystal growth via tethered peptides or synthetic extracellular matrices. Rather, they aim to advance our understanding of natural biodeposition, use the insights gained to grow pyrite materials and devices.</p>
<p> </p>
INSPIRE_Pyrite
largerWorkCitation
project
eng; USA
biota
oceans
2016-02-09
0
BCO-DMO catalogue of parameters from Effects of temperature on biomass and sulfide production in Desulfovibrio hydrothermals (INSPIRE_Pyrite project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/638098.rdf
Name: phase
Units: text
Description: <p>growth phase - exponential or stationary</p>
http://lod.bco-dmo.org/id/dataset-parameter/638099.rdf
Name: temp
Units: degrees Celsius
Description: <p>temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/638100.rdf
Name: numb_cells_t0
Units: cells per milliliter
Description: <p>number of cells at time = 0 (beginning)</p>
http://lod.bco-dmo.org/id/dataset-parameter/638101.rdf
Name: numb_cells_tend
Units: cells per milliliter
Description: <p>number of cells at time = end (of experiment)</p>
http://lod.bco-dmo.org/id/dataset-parameter/638102.rdf
Name: max_sulfide_prod
Units: milliMoles
Description: <p>maximum sulfide concentration produced</p>
http://lod.bco-dmo.org/id/dataset-parameter/638103.rdf
Name: std_error_prod
Units: milliMoles
Description: <p>standard error of maximum sulfide concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/638104.rdf
Name: max_sulfide_prod_rate
Units: milliMoles per hour
Description: <p>maximum sulfide production rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/638105.rdf
Name: std_error_rate
Units: milliMoles per hour
Description: <p>standard error of maximum sulfide production rate</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
1288
https://datadocs.bco-dmo.org/file/QAAXx3ktXVVyBV/DhydroBioProd.csv
DhydroBioProd.csv
Primary data file for dataset ID 638091
download
https://osprey.bco-dmo.org/dataset/638091/data/download
download
onLine
dataset
<p>Inoculum: 200 µl stock culture (stationary phase) into 50 ml medium (expected at t0: 8.0 E+5 cells/ml).</p>
<p>"The time between t0 and tend is variable.&nbsp; We wait to reach the stationary phase.&nbsp; The rate is the maximum rate (exponential phase of sulfide production)." A. Picard, personal communication.<br />
&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>Method for cell counting:</strong> Cell cultures were fixed with 3.7% formaldehyde for cell counts. Between 100 and 1,000 microliters of fixed sample were filtered onto a 0.2 µm GTBP polycarbonate filter (Millipore), stained with DAPI (4’,6’-diamidino-2-phenylindole; Sigma), and counted via epiflourescent microscopy, using a Zeiss Axiophot scope equipped with objectives capable of 20x, 60x and 100x magnification.</p>
<p><strong>Method for sulfide concentration: </strong>Spectrophotometric quantification using standard curve after&nbsp; <a href="http://onlinelibrary.wiley.com/doi/10.4319/lo.1969.14.3.0454/pdf" target="_blank">Cline, 1969.</a></p>
<p>adapted to the range of concentrations in the cultures.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Epifluorescence Microscope - Zeiss Axiophot
Epifluorescence Microscope - Zeiss Axiophot
PI Supplied Instrument Name: Epifluorescence Microscope - Zeiss Axiophot PI Supplied Instrument Description:Light microscope equipped for bright field (both transmitted and reflected), phase contrast, transmitted and reflected polarization and Nomarski differential interference contrast microscopy, as well as epifluorescence.
Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/
spectrophotometer
spectrophotometer
PI Supplied Instrument Name: spectrophotometer Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/