http://lod.bco-dmo.org/id/dataset/932220
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
2024-07-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Physiology responses to experimental iron warming interactions of coastal and oceanic Synechococcus collected from the South China Sea
2025-05-03
publication
2025-05-03
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-05-16
publication
https://doi.org/10.26008/1912/bco-dmo.932220.1
David A. Hutchins
University of Southern California
principalInvestigator
Feixue Fu
University of Southern California
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: Duan, R., Hutchins, D. A., Fu, F. (2025) Physiology responses to experimental iron warming interactions of coastal and oceanic Synechococcus collected from the South China Sea. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-05-03 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.932220.1 [access date]
Physiology responses of coastal and oceanic Synechococcus to iron warming interactions Dataset Description: Methods and Sampling: <p><strong>Culturing Conditions and experimental design</strong></p>
<p><em>Synechococcus</em>&nbsp;strains XM24 and YX 04-1 were isolated from the coastal region and offshore water of the South China Sea, respectively (Schiksnis et al., 2024; Zheng et al., 2018). Phylogenetic analysis classified them into subclade II clade CB5 and subclade I clade II, respectively.</p>
<p>The cultures were grown in Aquil medium using trace metal clean artificial seawater (Sunda et al., 2005). The experiments were conducted using a matrix of two Fe concentrations (2 nM and 250 nM) and two temperatures (24℃ and 27℃) under a 12:12 dark/light cool-white fluorescent light with an intensity of ~30 μmol quanta m<sup>-2</sup>&nbsp;s<sup>-1</sup>. The cultures were isolated at ~25C, and hence 24℃ and 27℃ were used in the experiments to bracket this ambient temperature. A semi-continuous approach (Yang et al., 2021) was employed to grow the cultures under each treatment condition for at least two months (12 generations or more) prior to measuring physiological responses and collecting RNA samples. The cultures were diluted every other day based on in vivo fluorescence readings.&nbsp;For each dilution, initial and final in vivo fluorescence were measured and&nbsp;growth rates were calculated to ensure cultures remained in exponential phase. Physiological parameters determined included growth rates, chlorophyll a, Fe quotas and carbon fixation rates. RNA samples were flash-frozen and stored in liquid nitrogen until extraction and sequencing.</p>
<p>To compare and contrast the responses of both isolates to warming and Fe limitation individually and in combination, six-treatment comparisons were conducted: 1)&nbsp;-Fe@27<sup>o</sup>C: Fe-limited vs Fe-replete at 27<sup>o</sup>C; 2)&nbsp;-Fe@24<sup>o</sup>C: Fe-limited vs Fe-replete at 24<sup>o</sup>C; 3)&nbsp;-Fe/warming interaction (-Fe+warming): 27<sup>o</sup>C Fe-limited vs 24<sup>o</sup>C Fe-replete; 4)&nbsp;27<sup>o</sup>C@+Fe: 27<sup>o</sup>C Fe-replete vs 24<sup>o</sup>C Fe-replete; 5)&nbsp;27C@-Fe: 27<sup>o</sup>C Fe-limited vs 24<sup>o</sup>C Fe-limited; 6)&nbsp;+Fe/warming interaction (+Fe+warming): Fe-replete at 27<sup>o</sup>C vs Fe-limited at 24<sup>o</sup>C.</p>
<p><strong>Growth rates, Carbon fixation rates and elemental stoichiometry</strong></p>
<p>Cell growth rates were determined by measuring in vivo fluorescence every other day, using the equation μ=ln(N/N<sub>0</sub>)/(t-t<sub>0</sub>), where N represented the final cellular in vivo fluorescence at time t, and N<sub>0</sub>&nbsp;represented the initial in vivo fluorescence at time t<sub>0</sub>. Carbon fixation rates were assessed using&nbsp;<sup>14</sup>C-labeled bicarbonate. Specifically, 50 mL cultures were extracted from each bottle, incubated with&nbsp;<sup>14</sup>C for 3 hours, and then filtered onto GF/F membranes. Subsequently,&nbsp;<sup>14</sup>C radioactivity of the filters was measured using a Beckman System 6500 liquid scintillation counter, converted to carbon fixation rates and normalized to particulate organic carbon concentration (Fu et al., 2008). To determine the particulate organic carbon and nitrogen (POC and PON), the cultures were filtered onto pre-combusted glass microfiber filters. The filters were then dried in an oven and analyzed using a Costech Elemental Analyzer that was calibrated with methionine and acetanilide (Fu et al., 2008).</p>
<p><strong>Fe quota measurements</strong></p>
<p>To obtain iron quota results, cell samples were filtered, digested, and analyzed by mass spectrometry following published methods (Hawco et al., 2020; Yang et al., 2021). Briefly, cultures were filtered using acid-washed 0.2 μm Supor polyethersulfone filters and rinsed with an oxalate reagent to eliminate extracellular trace metals (Kustka et al., 2003). The filters were digested with 5 ml of 50% nitric acid (HNO<sub>3</sub>) at 95°C for five days in 30 mL perfluoroalkoxy vials (Savillex). After removing the filters and drying the samples at 100°C, they were resolubilized in 200 μL of 1:1 concentrated HNO<sub>3</sub>&nbsp;and hydrochloric acid (HCl), sealed and heated for approximately 2-3 hours. The samples were dried down again and then resuspended in 5 mL of 0.1 M distilled HNO<sub>3</sub>&nbsp;for Fe and P concentration analysis using a Thermo Scientific Element2 inductively coupled plasma mass spectrometry (ICP-MS). The cellular Fe quota was represented by the Fe concentration normalized to phosphate concentration and POC &nbsp;(Kustka et al., 2003).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851222 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851222
completed
David A. Hutchins
University of Southern California
213-740-5616
Department of Biological Sciences 3616 Trousdale Parkway, AHF 20
Los Angeles
CA
90089
USA
dahutch@usc.edu
pointOfContact
Feixue Fu
University of Southern California
2137403188
Department of Biology, MC 0371, University of Southern California 3616 Trousdale Pkwy
Los Angeles
CA
90089
USA
ffu@usc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
Strain
Temperature
Fe_concentration
Fe_C
C_fixation
PON
Fe_P
POC
Costech Elemental Analyzer ECS 4010
Thermo Scientific Element2 inductively coupled plasma mass spectrometry (ICP-MS)
Beckman System 6500 liquid scintillation counter
10-AU Fluorometer (Turner Designs)
theme
None, User defined
sample identification
sample description
temperature of sample or a generic measurement (not in-situ water temp)
treatment
Iron
No BCO-DMO term
particulate organic nitrogen
particulate organic Carbon (POC)
featureType
BCO-DMO Standard Parameters
Costech International Elemental Combustion System (ECS) 4010
Inductively Coupled Plasma Mass Spectrometer
Liquid Scintillation Counter
Turner Designs Fluorometer 10-AU
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.
Collaborative Research: Evolutionary, biochemical and biogeochemical responses of marine cyanobacteria to warming and iron limitation interactions
https://osprey.bco-dmo.org/project/786679
Collaborative Research: Evolutionary, biochemical and biogeochemical responses of marine cyanobacteria to warming and iron limitation interactions
<p>NSF abstract:<br />
The oceans absorb much of the heat generated by human activities, and this warming of the surface ocean has consequences for important groups of marine organisms. Marine cyanobacteria are one such key group of organisms, since they supply much of the essential carbon and nitrogen that supports nearly all the rest of the marine food web. Currently, the growth of cyanobacteria is mostly constrained by scarce supplies of the micronutrient element iron, but they are also very sensitive to the ongoing increases in seawater temperature. Preliminary results suggest that warming could partly mitigate the negative effects of iron limitation on marine cyanobacteria. This project examines in depth how these interactions between warming and iron limitation will affect the future ocean carbon and nitrogen cycles, using laboratory culture experiments showing how cyanobacteria respond to simultaneously changing temperature and iron supplies. Both short-term response studies and long-term evolutionary experiments testing for adaptation use a comprehensive set of molecular biology tools targeting genes to proteins. The final goal is to apply the results of these experiments to improve quantitative models predicting how the ocean's carbon and nitrogen cycles, biological productivity, and living resources will respond to a warming future climate. Two graduate students, a postdoc and 3-4 underrepresented undergraduate researchers are supported, and the investigators also mentor summer science interns from largely Hispanic local high schools.</p>
<p>The physiology, biochemistry and biogeography of nitrogen-fixing cyanobacteria and unicellular picocyanobacteria are strongly influenced by temperature, subjecting them to intense selective pressure as the modern ocean steadily warms up. These groups have likewise been rigorously selected under chronic iron (Fe) scarcity, and the availability of this crucial micronutrient is also changing with a shifting climate. This project examines short-term acclimation and long-term evolutionary responses of Fe-stressed marine cyanobacteria to a warmer environment. Preliminary data show that Iron Use Efficiencies (IUE, mols N fixed.hr-1 mol cellular Fe-1) of Fe-limited Trichodesmium increase 4 to 5-fold with a 5oC temperature increase, allowing the cells to much more efficiently leverage scarce available Fe supplies to grow and fix nitrogen. This means that warming can to a large degree mitigate the negative effects of Fe limitation on Trichodesmium, resulting in a modelled 22% increase in global nitrogen fixation by 2100 in a warmer climate. This project aims to uncover the cellular biochemical mechanisms involved in this Fe-limitation/thermal IUE effect in a four-year experimental evolution study of the diazotrophs Trichodesmium and Crocosphaera and the picocyanobacteria Synechococcus and Prochlorococcus, under a multi-variate selection matrix of temperature and Fe availability. The objectives are to 1) Assess the long-term adaptive responses of fitness, IUE and physiology to Fe limitation and warming interactions in these four major cyanobacterial groups; 2) Determine the molecular and biochemical mechanisms behind the surprising Fe/warming interactive effect on IUE using genomics, transcriptomics and quantitative proteomics coupled with 'metalloproteomics' determinations of Fe content in critical proteins; 3) Compare and contrast acclimation and adaptation responses to Fe limitation and warming in key cyanobacteria taxa, and 4) Integrate results using a published biogeochemical modeling approach to assess global consequences for marine productivity and nitrogen fixation. This project offers a mechanistic and predictive understanding of adaptation to Fe and warming co-stressors in a rapidly changing future ocean environment for some of the most important photoautotrophic functional groups in the ocean.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Cyanobacteria Warming Responses
largerWorkCitation
project
eng; USA
oceans
112
118
17
24
2020-07-01
2020-12-31
0
BCO-DMO catalogue of parameters from Physiology responses to experimental iron warming interactions of coastal and oceanic Synechococcus collected from the South China Sea
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/955362.rdf
Name: Sample_ID
Units: unitless
Description: <p>Unique identifier for samples receiving treatment</p>
http://lod.bco-dmo.org/id/dataset-parameter/955363.rdf
Name: Strain
Units: unitless
Description: <p>Strain of Synechococcus sample receiving treatment</p>
http://lod.bco-dmo.org/id/dataset-parameter/955364.rdf
Name: Temperature
Units: degrees Celsius
Description: <p>Temperature applied to sample receiving treatment</p>
http://lod.bco-dmo.org/id/dataset-parameter/955365.rdf
Name: Fe_concentration
Units: nM
Description: <p>Iron concentration applied to sample receiving treatment</p>
http://lod.bco-dmo.org/id/dataset-parameter/955366.rdf
Name: Fe_C
Units: nmol/umol
Description: <p>Cellular iron (nmol) quota normalized to cellular carbon (umol)</p>
http://lod.bco-dmo.org/id/dataset-parameter/955367.rdf
Name: C_fixation
Units: h⁻¹
Description: <p>Carbon fixation rates per hour</p>
http://lod.bco-dmo.org/id/dataset-parameter/955368.rdf
Name: PON
Units: pmol N cell⁻¹
Description: <p>Particulate organic nitrogen per day</p>
http://lod.bco-dmo.org/id/dataset-parameter/955369.rdf
Name: Fe_P
Units: mmol/mol
Description: <p>Cellular iron (mmol) quota normalized to cellular phosphorus (mol)</p>
http://lod.bco-dmo.org/id/dataset-parameter/955370.rdf
Name: POC
Units: pmol C cell⁻¹
Description: <p>Particulate organic nitrogen per day</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
2201
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/1ac6e645-5dc4-4156-be5c-6ca2007225c5/content
download
https://doi.org/10.26008/1912/bco-dmo.932220.1
download
onLine
dataset
<p><strong>Culturing Conditions and experimental design</strong></p>
<p><em>Synechococcus</em>&nbsp;strains XM24 and YX 04-1 were isolated from the coastal region and offshore water of the South China Sea, respectively (Schiksnis et al., 2024; Zheng et al., 2018). Phylogenetic analysis classified them into subclade II clade CB5 and subclade I clade II, respectively.</p>
<p>The cultures were grown in Aquil medium using trace metal clean artificial seawater (Sunda et al., 2005). The experiments were conducted using a matrix of two Fe concentrations (2 nM and 250 nM) and two temperatures (24℃ and 27℃) under a 12:12 dark/light cool-white fluorescent light with an intensity of ~30 μmol quanta m<sup>-2</sup>&nbsp;s<sup>-1</sup>. The cultures were isolated at ~25C, and hence 24℃ and 27℃ were used in the experiments to bracket this ambient temperature. A semi-continuous approach (Yang et al., 2021) was employed to grow the cultures under each treatment condition for at least two months (12 generations or more) prior to measuring physiological responses and collecting RNA samples. The cultures were diluted every other day based on in vivo fluorescence readings.&nbsp;For each dilution, initial and final in vivo fluorescence were measured and&nbsp;growth rates were calculated to ensure cultures remained in exponential phase. Physiological parameters determined included growth rates, chlorophyll a, Fe quotas and carbon fixation rates. RNA samples were flash-frozen and stored in liquid nitrogen until extraction and sequencing.</p>
<p>To compare and contrast the responses of both isolates to warming and Fe limitation individually and in combination, six-treatment comparisons were conducted: 1)&nbsp;-Fe@27<sup>o</sup>C: Fe-limited vs Fe-replete at 27<sup>o</sup>C; 2)&nbsp;-Fe@24<sup>o</sup>C: Fe-limited vs Fe-replete at 24<sup>o</sup>C; 3)&nbsp;-Fe/warming interaction (-Fe+warming): 27<sup>o</sup>C Fe-limited vs 24<sup>o</sup>C Fe-replete; 4)&nbsp;27<sup>o</sup>C@+Fe: 27<sup>o</sup>C Fe-replete vs 24<sup>o</sup>C Fe-replete; 5)&nbsp;27C@-Fe: 27<sup>o</sup>C Fe-limited vs 24<sup>o</sup>C Fe-limited; 6)&nbsp;+Fe/warming interaction (+Fe+warming): Fe-replete at 27<sup>o</sup>C vs Fe-limited at 24<sup>o</sup>C.</p>
<p><strong>Growth rates, Carbon fixation rates and elemental stoichiometry</strong></p>
<p>Cell growth rates were determined by measuring in vivo fluorescence every other day, using the equation μ=ln(N/N<sub>0</sub>)/(t-t<sub>0</sub>), where N represented the final cellular in vivo fluorescence at time t, and N<sub>0</sub>&nbsp;represented the initial in vivo fluorescence at time t<sub>0</sub>. Carbon fixation rates were assessed using&nbsp;<sup>14</sup>C-labeled bicarbonate. Specifically, 50 mL cultures were extracted from each bottle, incubated with&nbsp;<sup>14</sup>C for 3 hours, and then filtered onto GF/F membranes. Subsequently,&nbsp;<sup>14</sup>C radioactivity of the filters was measured using a Beckman System 6500 liquid scintillation counter, converted to carbon fixation rates and normalized to particulate organic carbon concentration (Fu et al., 2008). To determine the particulate organic carbon and nitrogen (POC and PON), the cultures were filtered onto pre-combusted glass microfiber filters. The filters were then dried in an oven and analyzed using a Costech Elemental Analyzer that was calibrated with methionine and acetanilide (Fu et al., 2008).</p>
<p><strong>Fe quota measurements</strong></p>
<p>To obtain iron quota results, cell samples were filtered, digested, and analyzed by mass spectrometry following published methods (Hawco et al., 2020; Yang et al., 2021). Briefly, cultures were filtered using acid-washed 0.2 μm Supor polyethersulfone filters and rinsed with an oxalate reagent to eliminate extracellular trace metals (Kustka et al., 2003). The filters were digested with 5 ml of 50% nitric acid (HNO<sub>3</sub>) at 95°C for five days in 30 mL perfluoroalkoxy vials (Savillex). After removing the filters and drying the samples at 100°C, they were resolubilized in 200 μL of 1:1 concentrated HNO<sub>3</sub>&nbsp;and hydrochloric acid (HCl), sealed and heated for approximately 2-3 hours. The samples were dried down again and then resuspended in 5 mL of 0.1 M distilled HNO<sub>3</sub>&nbsp;for Fe and P concentration analysis using a Thermo Scientific Element2 inductively coupled plasma mass spectrometry (ICP-MS). The cellular Fe quota was represented by the Fe concentration normalized to phosphate concentration and POC &nbsp;(Kustka et al., 2003).</p>
Specified by the Principal Investigator(s)
<p>The significance of the physiological parameters between Fe and temperature changes was assessed via two-way ANOVA and a Tukey multiple comparison test at p-value&lt;0.05 in Graphpad prism v9.5.1, including growth rates, Fe quota, and carbon fixation rates.&nbsp;</p>
Specified by the Principal Investigator(s)
- Submitted dataset contained two tables, one for each strain
- Imported "Duan_Syn_physiology.xlsx" into BCO-DMO system twice
- Combined the data from both tables
- Added field "Strain" to represent the difference in the tables
- Added values for the treatments of iron and temperature
- Renamed fields to comply with BCO-DMO best practices
- Applied consistent formatting of identifiers
- Exported file as "932220_v1_synechococcus_iron_warming"
Specified by BCO-DMO Data Managers
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
Costech Elemental Analyzer ECS 4010
Costech Elemental Analyzer ECS 4010
PI Supplied Instrument Name: Costech Elemental Analyzer ECS 4010 Instrument Name: Costech International Elemental Combustion System (ECS) 4010 Instrument Short Name:Costech ECS 4010 Instrument Description: The ECS 4010 Nitrogen / Protein Analyzer is an elemental combustion analyser for CHNSO elemental analysis and Nitrogen / Protein determination. The GC oven and separation column have a temperature range of 30-110 degC, with control of +/- 0.1 degC.
Thermo Scientific Element2 inductively coupled plasma mass spectrometry (ICP-MS)
Thermo Scientific Element2 inductively coupled plasma mass spectrometry (ICP-MS)
PI Supplied Instrument Name: Thermo Scientific Element2 inductively coupled plasma mass spectrometry (ICP-MS) 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/
Beckman System 6500 liquid scintillation counter
Beckman System 6500 liquid scintillation counter
PI Supplied Instrument Name: Beckman System 6500 liquid scintillation counter Instrument Name: Liquid Scintillation Counter Instrument Short Name:LSC Instrument Description: Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used to quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.
Liquid scintillation counters are instruments assaying alpha and beta radiation by quantitative detection of visible light produced by the passage of rays or particles through a suitable scintillant incorporated into the sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB21/
10-AU Fluorometer (Turner Designs)
10-AU Fluorometer (Turner Designs)
PI Supplied Instrument Name: 10-AU Fluorometer (Turner Designs) Instrument Name: Turner Designs Fluorometer 10-AU Instrument Short Name:Turner Fluorometer 10-AU Instrument Description: The Turner Designs 10-AU Field Fluorometer is used to measure Chlorophyll fluorescence. The 10AU Fluorometer can be set up for continuous-flow monitoring or discrete sample analyses. A variety of compounds can be measured using application-specific optical filters available from the manufacturer (read more from Turner Designs, turnerdesigns.com, Sunnyvale, CA, USA). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0393/