http://lod.bco-dmo.org/id/dataset/858743
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
2021-08-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Growth rates of the polar diatom Chaetoceros RS19 under various +Zn and +Co conditions from September 2019 (MM Saito project)
2021-08-31
publication
2021-08-31
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-09-20
publication
https://doi.org/10.26008/1912/bco-dmo.858743.1
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) Growth rates of the polar diatom Chaetoceros RS19 under various +Zn and +Co conditions from September 2019 (MM Saito project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-08-31 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.858743.1 [access date]
Growth rates of the Ross Sea diatom isolate Chaetoceros sp. RS19 under various Zinc and Cobalt additions. Dataset Description: <p>Growth rates of the Ross Sea diatom isolate Chaetoceros sp. RS19 under various Zn and Co additions.</p> Methods and Sampling: <p><strong>Methodology:</strong></p>
<p><strong>Sampling and analytical procedures:&nbsp;</strong></p>
<p><em>Media and culturing techniques</em></p>
<p><em>Chaetoceros</em> RS19 cultures were maintained in a 4°C incubator under constant fluorescent lighting (30 µmol photon m<sup>-2</sup> s<sup>-1</sup>). All cultures were randomly repositioned each day to avoid any effect of subtle variation in light intensity on growth. <em>Chaetoceros </em>RS19 was originally isolated by D. Moran from the Ross Sea, Antarctica, and cultures were maintained in the Saito laboratory culture collection at the Woods Hole Oceanographic Institution. All cultures were axenic and maintained by sterile technique until needed. Polycarbonate and plastic bottles were cleaned to remove trace metal contaminants before use. This procedure involved, at minimum, a 72h soak in &lt;1% Citranox detergent, five rinses in Mili-Q water, a 7 day soak in 10% HCl, and five rinses with dilute acid (HCl, pH 2). Cultures were grown in microwave-sterilized 28 mL polycarbonate centrifuge tubes and all solutions were pipetted after a tip rinse procedure consisting of three rinses with 10% HCl followed by three rinses with sterile dilute HCl (pH 2). All culture work was conducted in a Class 100 clean room and transferring of cultures was conducted in a laminar flow hood within the clean room.</p>
<p>Culture media was prepared after that used by Sunda and Huntsman for trace metal experimentation (Sunda and Huntsman 1995). Microwave sterilized, 0.2 µm-filtered Equatorial Pacific surface seawater collected at station 14 of the 2016 ProteOMZ expedition (10.5600°S, 146.3133° W; cruise code FK160115) was used as the media base. Macronutrients were added to this sterile base to a final concentration of 88.2 µM NaNO<sub>3</sub>, 41.5 µM NaH<sub>2</sub>PO<sub>4</sub>, and 106 µM Na<sub>2</sub>SiO<sub>3</sub> and were chelexed before use. Added vitamins included 2 nM biotin, 0.37 nM B<sub>12</sub> as cyanocobalamin, and 300 nM thiamine and were also chelexed before use. Trace metals were added to final media concentrations of 10<sup>-7</sup> M FeCl<sub>3</sub>, 4.8 x 10<sup>-8</sup> M MnCl<sub>2</sub>, 4.0 x 10<sup>-8</sup> M CuSO<sub>4</sub>, 10<sup>-7</sup> M NiCl<sub>2</sub>, and 10<sup>-8</sup> M Na<sub>2</sub>O<sub>3</sub>Se within a 10<sup>-4</sup> M ethylenediamine tetraacetic acid disodium salt (EDTA, Acros Organics, C<sub>10</sub>H<sub>14</sub>N<sub>2</sub>Na<sub>2</sub>O<sub>8</sub>) metal ion buffer system. All media amendments were sterile filtered through acid-rinsed 0.2 µm filters before addition to final media, and final media equilibrated for at least 12h before inoculation.</p>
<p>Established cultures were first acclimated in low-metal media containing 1 nM total added Zn or less for at least three transfers. These acclimated cultures were used to inoculate initial cultures at 1% volume. All growth media was chilled at 4°C prior to inoculation. Zn or Co limitation experiments were first performed using a range of added Zn concentrations with Co omitted and vice versa. We refer to growth rate experiments using media amended with Zn <em>or</em> Co (while omitting the other) as “simple limitation” experiments. Growth rate experiments in which one metal was held at a constant total added value while varying the added concentration of the other metal were also conducted—we refer to these as “double addition” experiments. Growth of all experiment cultures was monitored by relative chlorophyll fluorescence using a Turner TD-700 fluorometer, calibrated prior to measurement with a solid standard. All cultures were grown in 28 mL acid cleaned, microwave sterilized polycarbonate tubes (Nalgene) that are compatible with the fluorometer, which enabled measurements to be taken without exposing cultures to contaminating metals. Growth rates were calculated as the slope of the natural logarithm of the increase in chlorophyll fluorescence over a four-measurement (usually 4 day) period during exponential growth. Computed ratios of [Zn<sup>2+</sup>] and [Co<sup>2+</sup>] to total concentrations, whose values are 10<sup>-3.99</sup> and 10<sup>-3.63 </sup>respectively, were used to convert total added metal concentrations to free ion concentrations and are the same as those used by Sunda and Huntsman (Sunda and Huntsman 1995).</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
Experiment_Type
Added_Zn
Added_Co
Total_Zn
Total_Co
log_Zn2plus
log_Co2plus
Growth_rate_replicate_A
Growth_rate_replicate_B
Growth_rate_average_base_value
Growth_rate_average_standard_deviation
Incubator
Turner Instruments TD-700 Fluorometer
theme
None, User defined
experiment type
treatment
trace metal concentration
Zinc
Cobalt
growth
standard deviation
featureType
BCO-DMO Standard Parameters
In-situ incubator
Turner Designs 700 Laboratory Fluorometer
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
2019-09-01
2019-09-30
0
BCO-DMO catalogue of parameters from Growth rates of the polar diatom Chaetoceros RS19 under various +Zn and +Co conditions from September 2019 (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/859455.rdf
Name: Experiment_Type
Units: unitless
Description: <p>One (simple) or both (double addition) metals added</p>
http://lod.bco-dmo.org/id/dataset-parameter/859456.rdf
Name: Added_Zn
Units: nanomoles per liter (nmol/L)
Description: <p>Total amount of added zinc (Zn) to incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/859457.rdf
Name: Added_Co
Units: nanomoles per liter (nmol/L)
Description: <p>Total amount of added cobalt (Co) to incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/859458.rdf
Name: Total_Zn
Units: nanomoles per liter (nmol/L)
Description: <p>Total zinc (Zn). Added Zn and background media Zn.</p>
http://lod.bco-dmo.org/id/dataset-parameter/859459.rdf
Name: Total_Co
Units: nanomoles per liter (nmol/L)
Description: <p>Total cobalt (Co). Added Co and background media Co.</p>
http://lod.bco-dmo.org/id/dataset-parameter/859460.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/859461.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/859462.rdf
Name: Growth_rate_replicate_A
Units: per day (d-1)
Description: <p>Growth rate of treatment replicate A</p>
http://lod.bco-dmo.org/id/dataset-parameter/859463.rdf
Name: Growth_rate_replicate_B
Units: per day (d-1)
Description: <p>Growth rate of treatment replicate B</p>
http://lod.bco-dmo.org/id/dataset-parameter/859464.rdf
Name: Growth_rate_average_base_value
Units: per day (d-1)
Description: <p>Average growth rate of replicates A and B</p>
http://lod.bco-dmo.org/id/dataset-parameter/859465.rdf
Name: Growth_rate_average_standard_deviation
Units: per day (d-1)
Description: <p>Standard deviation of average growth rate of replicates A and B (+/-)</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
1769
https://darchive.mblwhoilibrary.org/bitstream/1912/27572/1/dataset-858743_growth-rates-polar-diatom-chaetoceros-rs19-zn-and-co-incubation-studies__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.858743.1
download
onLine
dataset
<p><strong>Methodology:</strong></p>
<p><strong>Sampling and analytical procedures:&nbsp;</strong></p>
<p><em>Media and culturing techniques</em></p>
<p><em>Chaetoceros</em> RS19 cultures were maintained in a 4°C incubator under constant fluorescent lighting (30 µmol photon m<sup>-2</sup> s<sup>-1</sup>). All cultures were randomly repositioned each day to avoid any effect of subtle variation in light intensity on growth. <em>Chaetoceros </em>RS19 was originally isolated by D. Moran from the Ross Sea, Antarctica, and cultures were maintained in the Saito laboratory culture collection at the Woods Hole Oceanographic Institution. All cultures were axenic and maintained by sterile technique until needed. Polycarbonate and plastic bottles were cleaned to remove trace metal contaminants before use. This procedure involved, at minimum, a 72h soak in &lt;1% Citranox detergent, five rinses in Mili-Q water, a 7 day soak in 10% HCl, and five rinses with dilute acid (HCl, pH 2). Cultures were grown in microwave-sterilized 28 mL polycarbonate centrifuge tubes and all solutions were pipetted after a tip rinse procedure consisting of three rinses with 10% HCl followed by three rinses with sterile dilute HCl (pH 2). All culture work was conducted in a Class 100 clean room and transferring of cultures was conducted in a laminar flow hood within the clean room.</p>
<p>Culture media was prepared after that used by Sunda and Huntsman for trace metal experimentation (Sunda and Huntsman 1995). Microwave sterilized, 0.2 µm-filtered Equatorial Pacific surface seawater collected at station 14 of the 2016 ProteOMZ expedition (10.5600°S, 146.3133° W; cruise code FK160115) was used as the media base. Macronutrients were added to this sterile base to a final concentration of 88.2 µM NaNO<sub>3</sub>, 41.5 µM NaH<sub>2</sub>PO<sub>4</sub>, and 106 µM Na<sub>2</sub>SiO<sub>3</sub> and were chelexed before use. Added vitamins included 2 nM biotin, 0.37 nM B<sub>12</sub> as cyanocobalamin, and 300 nM thiamine and were also chelexed before use. Trace metals were added to final media concentrations of 10<sup>-7</sup> M FeCl<sub>3</sub>, 4.8 x 10<sup>-8</sup> M MnCl<sub>2</sub>, 4.0 x 10<sup>-8</sup> M CuSO<sub>4</sub>, 10<sup>-7</sup> M NiCl<sub>2</sub>, and 10<sup>-8</sup> M Na<sub>2</sub>O<sub>3</sub>Se within a 10<sup>-4</sup> M ethylenediamine tetraacetic acid disodium salt (EDTA, Acros Organics, C<sub>10</sub>H<sub>14</sub>N<sub>2</sub>Na<sub>2</sub>O<sub>8</sub>) metal ion buffer system. All media amendments were sterile filtered through acid-rinsed 0.2 µm filters before addition to final media, and final media equilibrated for at least 12h before inoculation.</p>
<p>Established cultures were first acclimated in low-metal media containing 1 nM total added Zn or less for at least three transfers. These acclimated cultures were used to inoculate initial cultures at 1% volume. All growth media was chilled at 4°C prior to inoculation. Zn or Co limitation experiments were first performed using a range of added Zn concentrations with Co omitted and vice versa. We refer to growth rate experiments using media amended with Zn <em>or</em> Co (while omitting the other) as “simple limitation” experiments. Growth rate experiments in which one metal was held at a constant total added value while varying the added concentration of the other metal were also conducted—we refer to these as “double addition” experiments. Growth of all experiment cultures was monitored by relative chlorophyll fluorescence using a Turner TD-700 fluorometer, calibrated prior to measurement with a solid standard. All cultures were grown in 28 mL acid cleaned, microwave sterilized polycarbonate tubes (Nalgene) that are compatible with the fluorometer, which enabled measurements to be taken without exposing cultures to contaminating metals. Growth rates were calculated as the slope of the natural logarithm of the increase in chlorophyll fluorescence over a four-measurement (usually 4 day) period during exponential growth. Computed ratios of [Zn<sup>2+</sup>] and [Co<sup>2+</sup>] to total concentrations, whose values are 10<sup>-3.99</sup> and 10<sup>-3.63 </sup>respectively, were used to convert total added metal concentrations to free ion concentrations and are the same as those used by Sunda and Huntsman (Sunda and Huntsman 1995).</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes:</strong></p>
<p>- Split columns to separate growth rate average from its standard deviation (separated by a plus-minus sign)</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
Incubator
Incubator
PI Supplied Instrument Name: Incubator PI Supplied Instrument Description:Chaetoceros RS19 cultures were maintained in a 4°C incubator under constant fluorescent lighting (30 µmol photon m-2 s-1). Instrument Name: In-situ incubator Instrument Short Name:in-situ incubator Instrument Description: A device on a ship or in the laboratory that holds water samples under controlled conditions of temperature and possibly illumination. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/82/
Turner Instruments TD-700 Fluorometer
Turner Instruments TD-700 Fluorometer
PI Supplied Instrument Name: Turner Instruments TD-700 Fluorometer PI Supplied Instrument Description:Growth of all experiment cultures was monitored by relative chlorophyll fluorescence using a Turner TD-700 fluorometer, calibrated prior to measurement with a solid standard. All cultures were grown in 28 mL acid cleaned, microwave sterilized polycarbonate tubes (Nalgene) that are compatible with the fluorometer, which enabled measurements to be taken without exposing cultures to contaminating metals. Growth rates were calculated as the slope of the natural logarithm of the increase in chlorophyll fluorescence over a four-measurement (usually 4 day) period during exponential growth. Instrument Name: Turner Designs 700 Laboratory Fluorometer Instrument Short Name:TD-700 Instrument Description: The TD-700 Laboratory Fluorometer is a benchtop fluorometer designed to detect fluorescence over the UV to red range. The instrument can measure concentrations of a variety of compounds, including chlorophyll-a and fluorescent dyes, and is thus suitable for a range of applications, including chlorophyll, water quality monitoring and fluorescent tracer studies. Data can be output as concentrations or raw fluorescence measurements. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0510/