http://lod.bco-dmo.org/id/dataset/859211
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
2021-08-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metal quotas (ratios of Metal:P) of the polar diatom Chaetoceros sp. RS19 in +Zn and +Co incubation studies from January 2020 (MM Saito project)
2021-08-30
publication
2021-08-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-09-20
publication
https://doi.org/10.26008/1912/bco-dmo.859211.1
Mak A. Saito
Woods Hole Oceanographic Institution
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: Kellogg, R., Saito, M. A. (2021) Metal quotas (ratios of Metal:P) of the polar diatom Chaetoceros sp. RS19 in +Zn and +Co incubation studies from January 2020 (MM Saito project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-08-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.859211.1 [access date]
Metal quotas of the Ross Sea diatom isolate Chaetoceros RS19 measured via ICP-MS after growth in +Zn+Co media amendments. Dataset Description: <p>Metal quotas (ratios of Metal:P) of the Ross Sea diatom isolate Chaetoceros RS19 measured via ICP-MS after growth in +Zn+Co media amendments.</p> Methods and Sampling: <p><strong>Methodology:</strong></p>
<p><strong>Sampling and analytical procedures:</strong></p>
<p><em>Metal quotas</em></p>
<p>Cellular&nbsp;metal&nbsp;quotas were measured by inductively coupled plasma mass spectrometry (ICP-MS). Biomass from replicate 25 mL double addition cultures of <em>Chaetoceros </em>RS19 were pooled upon entering stationary phase and were centrifuged at 11,000 RPM (14,610 x g) for 40 minutes at 4°C. The cell pellet was resuspended in ~1 mL media and transferred to an acid-cleaned microcentrifuge tube. Cultures were centrifuged again for 30 min at 14,100 RPM (13,336 x g) at 4°C before the supernatant was discarded. Half of the remaining cell pellet was acidified in 800 mL of 5% nitric acid (Optima) containing 1 ppb indium for at least seven days while the other half was retained for proteomic analysis. Solids were removed by centrifugation. No attempt was made to remove extracellular metals by washing cells with additional metal chelators in order to minimize processing blanks. Quota determinations therefore include contributions from both intracellular and extracellular pools. Process blank digestions containing acid but no cells were performed in parallel. Digests were diluted by a factor of 9 with 5% nitric acid 1 ppb indium solution before being analyzed in duplicate on a Thermo ICAP-Q plasma mass spectrometer calibrated to a multi-element standard curve (Spex Certiprep) over a range of 1 – 20 ppb. Samples were analyzed in KED mode after an 85s sample uptake window and element mass windows were scanned 3 times during measurements. The 1 ppb indium internal standard was used to correct for variation in sample delivery and plasma suppression between samples. Process blanks were subtracted from measured concentrations. Phosphorus concentrations were also measured by ICP-MS simultaneously and were calibrated to a standard curve ranging from 100 – 3,200 ppb using a 1 ppm certified P stock (Alfa Aesar Specpure). The seawater media base used for all growth experiments was similarly analyzed via ICP-MS using a 1:10 dilution of media base into 5% nitric acid 1 ppb indium and analyzed as above to determine background media concentrations of total Zn and Co (0.7 nmol L<sup>-1 </sup>and 0.1 nmol L<sup>-1</sup>, respectively).</p>
Funding provided by Gordon and Betty Moore Foundation: Marine Microbiology Initiative (MMI) Award Number: GBMF3782 Award URL: https://www.moore.org/grant-detail?grantId=GBMF3782
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1657766 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1657766
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1658030 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1658030
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1736599 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1736599
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1850719 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1850719
completed
Mak A. Saito
Woods Hole Oceanographic Institution
508-289-2393
266 Woods Hole Rd. MS #51 Watson Lab
Woods Hole
MA
02543
USA
msaito@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
log_Zn2plus
log_Co2plus
Growth_rate_average
FE_to_P_avg
MN_to_P_avg
NI_to_P_avg
CU_to_P_avg
ZN_to_P_avg
CD_to_P_avg
CO_to_P_avg
Centrifuge
Thermo ICAP-Q plasma mass spectrometer
theme
None, User defined
Intensity (relative ion abundance)
growth
mole_ratio
featureType
BCO-DMO Standard Parameters
Centrifuge
Inductively Coupled Plasma Mass Spectrometer
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.
Marine Microbiology Initiative
https://www.moore.org/initiative-strategy-detail?initiativeId=marine-microbiology-initiative
Marine Microbiology Initiative
A Gordon and Betty Moore Foundation Program.
Forging a new paradigm in marine microbial ecology:
Microbes in the ocean produce half of the oxygen on the planet and remove vast amounts of carbon dioxide, a greenhouse gas, from the atmosphere. Yet, we have known surprisingly little about these microscopic organisms. As we discover answers to some long-standing puzzles about the roles that marine microorganisms play in supporting the ocean’s food webs and driving global elemental cycles, we realized that we still need to learn much more about what these organisms do and how they do it—including how they evolved and contribute to our ocean's health and productivity.
The Marine Microbiology Initiative seeks to gain a comprehensive understanding of marine microbial communities, including their diversity, functions and behaviors; their ecological roles; and their origins and evolution. Our focus has been to enable researchers to uncover the principles that govern the interactions among microbes and that govern microbially mediated nutrient flow in the sea. To address these opportunities, we support leaders in the field through investigator awards, multidisciplinary team research projects, and efforts to create resources of broad use to the research community. We also support development of new instrumentation, tools, technologies and genetic approaches.
Through the efforts of many scientists from around the world, the initiative has been catalyzing new science through advances in methods and technology, and to reduce interdisciplinary barriers slowing progress. With our support, researchers are quantifying nutrient pools in the ocean, deciphering the genetic and biochemical bases of microbial metabolism, and understanding how microbes interact with one another. The initiative has five grant portfolios:
Individual investigator awards for current and emerging leaders in the field.
Multidisciplinary projects that support collaboration across disciplines.
New instrumentation, tools and technology that enable scientists to ask new questions in ways previously not possible.
Community resource efforts that fund the creation and sharing of data and the development of tools, methods and infrastructure of widespread utility.
Projects that advance genetic tools to enable development of experimental model systems in marine microbial ecology.
We also bring together scientists to discuss timely subjects and to facilitate scientific exchange.
Our path to marine microbial ecology was a confluence of new technology that could accelerate science and an opportunity to support a field that was not well funded relative to potential impact. Around the time we began this work in 2004, the life sciences were entering a new era of DNA sequencing and genomics, expanding possibilities for scientific research – including the nascent field of marine microbial ecology. Through conversations with pioneers inside and outside the field, an opportunity was identified: to apply these new sequencing tools to advance knowledge of marine microbial communities and reveal how they support and influence ocean systems.
After many years of success, we will wind down this effort and close the initiative in 2021. We will have invested more than $250 million over 17 years to deepen understanding of the diversity, ecological activities and evolution of marine microbial communities. Thanks to the work of hundreds of scientists and others involved with the initiative, the goals have been achieved and the field has been profoundly enriched; it is now positioned to address new scientific questions using innovative technologies and methods.
MMI
largerWorkCitation
program
Marine Microbial Investigator Award: Investigator Mak Saito
https://osprey.bco-dmo.org/project/786672
Marine Microbial Investigator Award: Investigator Mak Saito
<p>In support of obtaining deeper knowledge of major biogeochemically relevant proteins to inform a mechanistic understanding of global marine biogeochemical cycles.</p>
MM Saito
largerWorkCitation
project
eng; USA
oceans
177.12379
177.12379
-76.48338
-76.48338
2020-01-01
2020-01-31
0
BCO-DMO catalogue of parameters from Metal quotas (ratios of Metal:P) of the polar diatom Chaetoceros sp. RS19 in +Zn and +Co incubation studies from January 2020 (MM Saito 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/859777.rdf
Name: log_Zn2plus
Units: moles per liter (mol/L)
Description: <p>Log of calculated free Zn2+ ion concentration in media. [Zn2+]</p>
http://lod.bco-dmo.org/id/dataset-parameter/859778.rdf
Name: log_Co2plus
Units: moles per liter (mol/L)
Description: <p>Log of calculated free Co2+ ion concentration in media. [Co2+]</p>
http://lod.bco-dmo.org/id/dataset-parameter/859779.rdf
Name: Growth_rate_average
Units: per day (d-1)
Description: <p>Average growth rate of replicates A and B</p>
http://lod.bco-dmo.org/id/dataset-parameter/859780.rdf
Name: FE_to_P_avg
Units: unitless
Description: <p>Average ratio of iron (Fe) in millmoles to phosphorous (P) in moles. Fe (mmol):P(mol) quota.</p>
http://lod.bco-dmo.org/id/dataset-parameter/859781.rdf
Name: MN_to_P_avg
Units: unitless
Description: <p>Average ratio of manganese (Mn) in millmoles to phosphorous (P) in moles. Mn (mmol):P(mol) quota.</p>
http://lod.bco-dmo.org/id/dataset-parameter/859782.rdf
Name: NI_to_P_avg
Units: unitless
Description: <p>Average ratio of nickel (Ni) in millmoles to phosphorous (P) in moles. Ni (mmol):P(mol) quota.</p>
http://lod.bco-dmo.org/id/dataset-parameter/859783.rdf
Name: CU_to_P_avg
Units: unitless
Description: <p>Average ratio of copper (Cu) in millmoles to phosphorous (P) in moles. Cu (mmol):P(mol) quota.</p>
http://lod.bco-dmo.org/id/dataset-parameter/859784.rdf
Name: ZN_to_P_avg
Units: unitless
Description: <p>Average ratio of zinc (Zn) in millimoles to phosphorous (P) in moles. Zn (mmol):P(mol) quota.</p>
http://lod.bco-dmo.org/id/dataset-parameter/859785.rdf
Name: CD_to_P_avg
Units: unitless
Description: <p>Average ratio of cadmium (Cd) in micromoles to phosphorous (P) in moles. Cd (umol):P(mol) quota.</p>
http://lod.bco-dmo.org/id/dataset-parameter/859786.rdf
Name: CO_to_P_avg
Units: unitless
Description: <p>Average ratio of cobalt (Co) in millimoles to phosphorous (P) in moles. Co (mmol):P(mol) quota.</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
736
https://darchive.mblwhoilibrary.org/bitstream/1912/27571/1/dataset-859211_metal-quotas-ratios-metalp-chaetoceros-sp-rs19-zn-and-co-incubation-studies__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.859211.1
download
onLine
dataset
<p><strong>Methodology:</strong></p>
<p><strong>Sampling and analytical procedures:</strong></p>
<p><em>Metal quotas</em></p>
<p>Cellular&nbsp;metal&nbsp;quotas were measured by inductively coupled plasma mass spectrometry (ICP-MS). Biomass from replicate 25 mL double addition cultures of <em>Chaetoceros </em>RS19 were pooled upon entering stationary phase and were centrifuged at 11,000 RPM (14,610 x g) for 40 minutes at 4°C. The cell pellet was resuspended in ~1 mL media and transferred to an acid-cleaned microcentrifuge tube. Cultures were centrifuged again for 30 min at 14,100 RPM (13,336 x g) at 4°C before the supernatant was discarded. Half of the remaining cell pellet was acidified in 800 mL of 5% nitric acid (Optima) containing 1 ppb indium for at least seven days while the other half was retained for proteomic analysis. Solids were removed by centrifugation. No attempt was made to remove extracellular metals by washing cells with additional metal chelators in order to minimize processing blanks. Quota determinations therefore include contributions from both intracellular and extracellular pools. Process blank digestions containing acid but no cells were performed in parallel. Digests were diluted by a factor of 9 with 5% nitric acid 1 ppb indium solution before being analyzed in duplicate on a Thermo ICAP-Q plasma mass spectrometer calibrated to a multi-element standard curve (Spex Certiprep) over a range of 1 – 20 ppb. Samples were analyzed in KED mode after an 85s sample uptake window and element mass windows were scanned 3 times during measurements. The 1 ppb indium internal standard was used to correct for variation in sample delivery and plasma suppression between samples. Process blanks were subtracted from measured concentrations. Phosphorus concentrations were also measured by ICP-MS simultaneously and were calibrated to a standard curve ranging from 100 – 3,200 ppb using a 1 ppm certified P stock (Alfa Aesar Specpure). The seawater media base used for all growth experiments was similarly analyzed via ICP-MS using a 1:10 dilution of media base into 5% nitric acid 1 ppb indium and analyzed as above to determine background media concentrations of total Zn and Co (0.7 nmol L<sup>-1 </sup>and 0.1 nmol L<sup>-1</sup>, respectively).</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes:</strong></p>
<p>- Renamed fields to meet BCO-DMO naming conventions&nbsp;</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
Centrifuge
Centrifuge
PI Supplied Instrument Name: Centrifuge PI Supplied Instrument Description:Biomass from replicate 25 mL double addition cultures of Chaetoceros RS19 were pooled upon entering stationary phase and were centrifuged at 11,000 RPM (14,610 x g) for 40 minutes at 4°C. The cell pellet was resuspended in ~1 mL media and transferred to an acid-cleaned microcentrifuge tube. Cultures were centrifuged again for 30 min at 14,100 RPM (13,336 x g) at 4°C before the supernatant was discarded. Half of the remaining cell pellet was acidified in 800 mL of 5% nitric acid (Optima) containing 1 ppb indium for at least seven days while the other half was retained for proteomic analysis. Solids were removed by centrifugation. Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
Thermo ICAP-Q plasma mass spectrometer
Thermo ICAP-Q plasma mass spectrometer
PI Supplied Instrument Name: Thermo ICAP-Q plasma mass spectrometer PI Supplied Instrument Description:Process blank digestions containing acid but no cells were performed in parallel. Digests were diluted by a factor of 9 with 5% nitric acid 1 ppb indium solution before being analyzed in duplicate on a Thermo ICAP-Q plasma mass spectrometer calibrated to a multi-element standard curve (Spex Certiprep) over a range of 1 – 20 ppb. Samples were analyzed in KED mode after an 85s sample uptake window and element mass windows were scanned 3 times during measurements. Instrument Name: Inductively Coupled Plasma Mass Spectrometer Instrument Short Name:ICP Mass Spec Instrument Description: An ICP Mass Spec is an instrument that passes nebulized samples into an inductively-coupled gas plasma (8-10000 K) where they are atomized and ionized. Ions of specific mass-to-charge ratios are quantified in a quadrupole mass spectrometer. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB15/