http://lod.bco-dmo.org/id/dataset/649904
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
2016-06-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Trichodesmium growth rate and cell size related to pCO2 and nutrients from experiments conducted at the University of Southern California from 2011-2013 (HiCO2_AdaptCyano project)
2016-06-22
publication
2016-06-22
revision
BCO-DMO Linked Data URI
2016-06-22
creation
http://lod.bco-dmo.org/id/dataset/649904
David A. Hutchins
University of Southern California
principalInvestigator
Eric A. Webb
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: Hutchins, D. A., Webb, E. A. (2016) Trichodesmium growth rate and cell size related to pCO2 and nutrients from experiments conducted at the University of Southern California from 2011-2013 (HiCO2_AdaptCyano project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version Final) Version Date 2016-06-22 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/649904 [access date]
Trichodesmium growth rate and cell size related to pCO2 and nutrients Dataset Description: <p><em>Trichodesmium&nbsp;erythraeum</em>&nbsp;growth rates per day for all replicates in each treatment calculated from cell counts.&nbsp;<em>Trichodesmium&nbsp;erythraeum</em>&nbsp;was grown in biological triplicate under two CO2 regimes (380 and 750 uatm pCO2) and four different nutrient regimes (replete, phosphorus-limited,iron-limited, iron/phosphorus&nbsp;colimited).&nbsp;</p>
<p>These data were utilized in the following publications:</p>
<p>Walworth, N. G., Fu, F. X., Webb, E. A., Saito, M. A., Moran, D., Mcllvin, M. R. &amp; Hutchins, D. A. (2016a). Mechanisms of increased Trichodesmium fitness under iron and phosphorus co-limitation in the present and future ocean.&nbsp;<em>Nature Communications</em>,&nbsp;<em>7</em>, 12081. doi: 10.1038/ncomms12081</p>
<p>Walworth, N. G., Lee, M. D., Suffridge, C., Qu, P., Fu, F., Saito, M. A., ... &amp; Hutchins, D. A. (2018). Functional genomics and phylogenetic evidence suggest genus-wide cobalamin production by the globally distributed marine nitrogen fixer Trichodesmium.&nbsp;<em>Frontiers in Microbiology</em>,&nbsp;<em>9</em>, 189. doi: <a href="https://doi.org/10.3389/fmicb.2018.00189" target="_blank">10.3389/fmicb.2018.00189</a></p>
<p>Genetic&nbsp;sequences from the&nbsp;<em>Trichodesmium&nbsp;erythraeum&nbsp;</em>used in this experiment can be accessed at&nbsp;The National Center for Biotechnology Information (NCBI) under the BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA312342" target="_blank">PRJNA312342</a>.</p>
<p>Walworth, N. G., Lee, M. D., Fu, F. X., Hutchins, D. A., ... &amp; Webb, E. A.(2016b). Molecular and physiological evidence of genetic assimilation to high CO2 in the marine nitrogen fixer Trichodesmium.&nbsp;<em>Proceedings of the National Academy of Sciences</em>,&nbsp;<em>113</em>(47), E7367-E7374. doi:&nbsp;<a href="https://doi.org/10.1073/pnas.1605202113">10.1073/pnas.1605202113</a></p>
<p>Related Dataset:&nbsp;<a href="https://www.bco-dmo.org/dataset/649873" target="_blank">Trichodesmium proteomes and Hi CO2 adaptation</a></p> Methods and Sampling: <p>The following are excerpts from the Nature Communication paper Walworth et al. 2016a.&nbsp;Please refer to this reference for more details of the methodology used to generate these data.</p>
<p>"We grew the nitrogen-fixing cyanobacterium Trichodesmium for 1 year under Fe/P co-limitation following 7 years of both low and high CO2 selection. "</p>
<p>"Growth rates were calculated according to microscopic cell counts for reported&nbsp;values,&nbsp;or using&nbsp;<em>in vivo</em>&nbsp;chlorophyll fluorescence measurements with a Turner 10 AU fluorometer for semi-daily dilution calculations in real time during the experiments. Comparisons between cell counts and&nbsp;<em>in vivo</em>-based growth rates revealed no significant differences between the two methods of assessing biomass changes."&nbsp;</p>
<p>A picogram carbon/µm filament was used for all replicates in each treatment (cell size proxy).</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1260233 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1260233
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
Eric A. Webb
University of Southern California
213-740-7954
Department of Biological Sciences, Marine and Environmental Biology Section; Dornsife College of Letters, Arts, and Sciences 3616 Trousdale Parkway AHF 331
Los Angeles
CA
90089-0371
USA
eawebb@usc.edu
pointOfContact
asNeeded
Dataset Version: Final
Unknown
Treatments
Growth_rates
pg_C_per_um_filament
Turner 10 AU fluorometer
theme
None, User defined
treatment
growth
cell_size
featureType
BCO-DMO Standard Parameters
Turner Designs Fluorometer 10-AU
instrument
BCO-DMO Standard Instruments
lab_Webb_Hutchins_Fu
service
Deployment Activity
Southern California
place
Locations
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.
Adaptation of key N2-fixing cyanobacteria to changing CO2
https://osprey.bco-dmo.org/project/551230
Adaptation of key N2-fixing cyanobacteria to changing CO2
<p><em>Description from NSF award abstract:</em><br />
This study will employ a novel combination of experimental evolution techniques and state-of-the-art molecular methods to yield unique insights into adaptive changes in the keystone marine cyanobacteria <em>Trichodesmium</em> and <em>Crocosphaera</em> in response to selection by high CO2. Several studies have suggested that N2-fixation rates of the biogeochemically-critical cyanobacteria <em>Trichodesmium</em> and <em>Crocosphaera</em> may increase dramatically in the future high CO2 ocean, but these have all used the same limited set of cultured isolates and considered cells only briefly acclimated to elevated CO2. The investigator's new results, however, demonstrate that a broad diversity of high- and low-CO2 adapted ecotypes exists within each diazotroph genus. Furthermore, in a preliminary four year experimental evolution study with <em>Trichodesmium</em>, the PIs observed large adaptive responses following 500-700 generations of selection by high CO2- but in a completely unexpected way. All of the six replicate high CO2-adapted cell lines exhibited strong constitutive up-regulation of N2 fixation rates. These very elevated N2 fixation rates continued, even though the cultures have were switched back to low-CO2 conditions for many months. Expression of the nif operon and N assimilatory genes was also up-regulated in these cell lines, as is expression of many intergenic regions of the genome.</p>
<p><strong>The investigators hypothesize that constitutive up-regulation of cellular N2 fixation systems may be a common adaptive response of both <em>Trichodesmium</em> and <em>Crocosphaera</em> under extended selection by elevated CO2. This project will test this hypothesis in a four-year experimental evolution study to determine the adaptive responses of both high- and low-CO2 specialized ecotypes of these two diazotrophs to increased CO2.</strong></p>
<p>The investigators will grow representative high- and low-CO2 adapted ecotypes from each genus in well-replicated cell lines at 380 ppm and 750 ppm CO2 for up to 1000 generations. Periodically, they will perform "switch" experiments to measure N2 and CO2 fixation rates and growth rates of high CO2-selected cell lines grown briefly (one week) at low CO2, and vice versa. These switch experiments will allow screening for cell lines which exhibit adaptive changes in phenotypically-expressed rate parameters, such as those observed in the preliminary <em>Trichodesmium</em> study. Evolutionary mechanisms in the CO2-selected cell lines will be examined by comparison of changes in their genomes, transcriptomes, and proteomes over time relative to reference genomes, using frozen samples archived monthly during the preceding selection period. Examination of these molecular and biochemical changes will be coordinated with an in-depth array of physiological and biogeochemical analyses. This combined approach will allow an evaluation of potential adaptive mechanisms in diazotrophic cyanobacteria ranging from indel, duplication, single nucleotide polymorphism, and transposition mutations to altered putative non-coding RNA expression, protein expression, and post-translational protein modifications, and then allow the investigators to link these mechanisms directly with their potential impacts on ecosystem-level biogeochemical processes like N2 and CO2 fixation. Finally, the research team will determine how long term selection by high CO2 affects the iron and phosphorus requirements of <em>Trichodesmium </em>and <em>Crocosphaera</em>, since constitutive up-regulation of N2 fixation would also have major implications for limitation of diazotrophs by these two critical nutrients in the future high CO2 ocean.</p>
HiCO2_AdaptCyano
largerWorkCitation
project
eng; USA
biota
oceans
Southern California
2016-06-22
Culture study at the University of Southern California, Los Angeles
0
BCO-DMO catalogue of parameters from Trichodesmium growth rate and cell size related to pCO2 and nutrients from experiments conducted at the University of Southern California from 2011-2013 (HiCO2_AdaptCyano 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/686972.rdf
Name: Treatments
Units: micromoles;nanomoles;uatm
Description: <p>CO2 and Nutrient regimes replicated three times; +P and -P speak of non-limiting or limiting phosphorus (20 μM and 0.5 μM phosphate respectively); +Fe or -Fe speak of limiting or non-limiting iron (500 nM iron); 380 or 750 indicate the partial pressure of CO2</p>
http://lod.bco-dmo.org/id/dataset-parameter/686973.rdf
Name: Growth_rates
Units: reciprocal time - per day (d-1) - because the cell numbers cancel out
Description: <p>rates calculated from cell counts</p>
http://lod.bco-dmo.org/id/dataset-parameter/686974.rdf
Name: pg_C_per_um_filament
Units: picogram
Description: <p>Picogram carbon per micron filament for all replicates in each treatment (cell size proxy)</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
1398
https://datadocs.bco-dmo.org/file/0AAMnvMIgynErx/cell_physio_size.csv
cell_physio_size.csv
Primary data file for dataset ID 649904
download
https://osprey.bco-dmo.org/dataset/649904/data/download
download
onLine
dataset
<p>The following are excerpts from the Nature Communication paper Walworth et al. 2016a.&nbsp;Please refer to this reference for more details of the methodology used to generate these data.</p>
<p>"We grew the nitrogen-fixing cyanobacterium Trichodesmium for 1 year under Fe/P co-limitation following 7 years of both low and high CO2 selection. "</p>
<p>"Growth rates were calculated according to microscopic cell counts for reported&nbsp;values,&nbsp;or using&nbsp;<em>in vivo</em>&nbsp;chlorophyll fluorescence measurements with a Turner 10 AU fluorometer for semi-daily dilution calculations in real time during the experiments. Comparisons between cell counts and&nbsp;<em>in vivo</em>-based growth rates revealed no significant differences between the two methods of assessing biomass changes."&nbsp;</p>
<p>A picogram carbon/µm filament was used for all replicates in each treatment (cell size proxy).</p>
<p>&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
Turner 10 AU fluorometer
Turner 10 AU fluorometer
PI Supplied Instrument Name: Turner 10 AU fluorometer 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/
Deployment: lab_Webb_Hutchins_Fu
lab_Webb_Hutchins_Fu
Webb-Hutchins-Fu USC
laboratory
Webb-Hutchins-Fu USC
laboratory