http://lod.bco-dmo.org/id/dataset/641495
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
2016-03-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
The abundance of Prochlorococcus cells containing the nitrate reductase gene (narB) at the HOT and BATS sites in the Pacific and Atlantic Oceans between October 2005 and January 2008
2016-03-31
publication
2016-03-31
revision
National Oceanographic Data Center (NODC)
2026-05-02
publication
http://accession.nodc.noaa.gov/
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2016-04-04
publication
https://doi.org/10.1575/1912/bco-dmo.641735
Sallie W. Chisholm
Massachusetts Institute of Technology
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: Chisholm, S. (2016) The abundance of Prochlorococcus cells containing the nitrate reductase gene (narB) at the HOT and BATS sites in the Pacific and Atlantic Oceans between October 2005 and January 2008. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version final) Version Date 2016-03-31 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.641735 [access date]
Abundance of Prochlorococcus cells containing gene narB at HOT and BATS Dataset Description: <p>Two year time series of the abundance of Prochlorococcus cells containing the nitrate reductase gene (narB) at the HOT and BATS sites in the Pacific and Atlantic Oceans. The goal was to collect long-term, high-resolution data on the temporal and spatial variability of Prochlorococcus narB genotypes belonging to the HLII and LLI clades. The abundance of Prochlorococcus cells containing narB for each of these clades was determined by quantitative PCR at 12 depths every month from October 2005 to December 2007 at two locations: BATS location (5 nautical mile radius around 31 40'N, 64 10'W) and HOT Station ALOHA (5 nautical mile radius around 22 45'N, 158 00' W). These field samples are a subset of those utilized in the "Prochlorococcus HOT/BATS" dataset (http://www.bco-dmo.org/dataset/3381).</p>
<p>These data are reported and described in:</p>
<pre>
Berube, P. M., Coe, A., Roggensack, S. E., & Chisholm, S. W. (2015). Temporal dynamics of Prochlorococcuscells with the potential for nitrate assimilation in the subtropical Atlantic and Pacific oceans. Limnology and Oceanography, 61(2), 482–495. doi:10.1002/lno.10226
</pre> Methods and Sampling: <p>Sample processing and analyses are detailed in the publications listed below. Briefly, 100ml of seawater was collected onto 25mm dia polycarbonate filters (0.22um pore size), rinsed with Tris-buffered saline, flash frozen in liquid N2, and stored at -80C until extraction. DNA was extracted using a combination of 5min of bead beating and 15min heat lysis at 95C. Extracted DNA was used as template of quantitative PCR reactions using primers specifically designed to target the narB gene from the HLII and LLI clades of Prochlorococcus. Standard curves used for quantitation of field data were derived from DNA extracted from defined cell numbers of cultured representatives of each clade.</p>
Funding provided by NSF Division of Biological Infrastructure (NSF DBI) Award Number: DBI-0424599 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0424599
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1153588 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1153588
Funding provided by Gordon and Betty Moore Foundation (GBMF) Award Number: GBMF495 Award URL: http://www.moore.org/grants/list/GBMF495
completed
Sallie W. Chisholm
Massachusetts Institute of Technology
(617) 253 1771
48-419 Department of Civil and Environmental Engineering 15 Vassar Street
Cambridge
MA
02139-4307
USA
chisholm@mit.edu
pointOfContact
asNeeded
Dataset Version: final
Unknown
gene
site
lat
lon
cruiseid
year
month
day
date
yrday_gmt
abundance
temp
sal
depth
sigma_0
standard_deviation
influx flow cytometer
theme
None, User defined
No BCO-DMO term
site
latitude
longitude
cruise id
year
month_gmt
day of month
date
day of year and decimal time (time zone GMT)
abundance
water temperature at measurement depth
salinity
depth
sigma-theta
standard deviation
featureType
BCO-DMO Standard Parameters
Flow Cytometer
instrument
BCO-DMO Standard Instruments
BATS_Prochlorococcus
HOT_Prochlorococcus
service
Deployment Activity
BATS at 31 40'N 64 10'W
100 km north of Oahu, Hawaii
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.
Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph
https://osprey.bco-dmo.org/project/522910
Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph
<p>Extracted from the NSF award abstract:</p>
<p>First discovered in 1988, Prochlorococcus is now recognized as the most abundant photosynthetic cell in the oceans and is responsible for a significant fraction of global primary productivity. Arguably one of the best studied marine microorganisms to date, Prochlorococcus is well-developed as a model system for advancing our understanding of microbial ecology. It is comprised of a collection of genetically and physiologically distinct populations that co-exist and are differentially distributed along quantifiable gradients of light, temperature, and inorganic nutrients. Early physiological studies using cultured isolates indicated that this group of cyanobacteria was unable to assimilate nitrate, typically the most abundant inorganic nitrogen source in the open ocean. This observation was supported by the first 12 genome sequences of Prochlorococcus which all lacked the genes necessary for nitrate assimilation. The lack of these genes in Prochlorococcus was puzzling given that closely related, and co-occurring, Synechococcus cells have them, and that nitrogen availability can be a significant limiting factor for primary production in marine ecosystems. Our understanding changed in 2009 with the discovery of nitrate assimilation genes in wild Prochlorococcus genomes and the isolation of an axenic strain capable of growth on nitrate (unpublished data). This discovery has lead to the overarching questions that are the subject of this project:</p>
<p>- What subset of the Prochlorococcus meta-population in the wild contains nitrate assimilation genes and how do the dynamics of this sub-population vary in time and space?</p>
<p>- What features of the environment select for cells with this functional trait? </p>
<p>- Is the phylogeny of Prochlorococcus nitrate assimilation genes better correlated with the local environment or the overall 16S-23S ITS phylogeny of Prochlorococcus?</p>
<p>- Do the genomes of cells that contain nitrate assimilation genes share specific features? What do they tell us about what other environmental variables influence the fitness of nitrate-assimilating cells?</p>
<p>- What are the physiological tradeoffs underlying the loss or gain of assimilation genes in particular strains?</p>
<p>These questions will be addressed using an integrative cross-scale approach to characterize nitrate assimilation by Prochlorococcus at the population, cellular, and genomic levels. Specifically, the distribution and abundance of nitrate assimilating Prochlorococcus will be measured at two contrasting open ocean time-series stations (HOT and BATS), and along a longitudinal gradient in the Atlantic (AMT). The PI will examine the regulation of nitrate assimilation, the kinetics of growth on nitrate, and the ability of Prochlorococcus to compete with Synechococcus under nitrogen limiting conditions. Further, they will use a culture independent single cell genomics approach to assess the phylogenetic diversity of nitrate assimilation genes within the genomic context of several ribotypes. These studies will advance our understanding the biogeography of functional traits in microbes, how it is shaped by selection, and the role of intra-species functional diversity in the overall population dynamics of Prochlorococcus.</p>
Prochloro_ecology
largerWorkCitation
project
eng; USA
oceans
BATS at 31 40'N 64 10'W; 100 km north of Oahu, Hawaii
-158
-64.1667
22.75
31.6667
2005-10-08
2008-01-31
BATS station (31.7 N 64.2 W) and HOT station ALOHA (22.75 N 158 W)
0
BCO-DMO catalogue of parameters from The abundance of Prochlorococcus cells containing the nitrate reductase gene (narB) at the HOT and BATS sites in the Pacific and Atlantic Oceans between October 2005 and January 2008
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/641505.rdf
Name: gene
Units: text
Description: <p>nitrate reductase gene (narB) in one of two clades (HLII and LLI)</p>
http://lod.bco-dmo.org/id/dataset-parameter/641506.rdf
Name: site
Units: text
Description: <p>Location of the measurement at one of two sites located at the HOT and BATS sites</p>
http://lod.bco-dmo.org/id/dataset-parameter/641507.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/641508.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/641509.rdf
Name: cruiseid
Units: numeric
Description: <p>The cruise identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/641510.rdf
Name: year
Units: unitless
Description: <p>Year the measurement was taken in YYYY format</p>
http://lod.bco-dmo.org/id/dataset-parameter/641511.rdf
Name: month
Units: mm
Description: <p>Month the measurement was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/641512.rdf
Name: day
Units: dd
Description: <p>Day the measurement was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/641513.rdf
Name: date
Units: mm/dd/yy
Description: <p>Date the sample was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/641514.rdf
Name: yrday_gmt
Units: decimal number
Description: <p>The year day the sample was taken with 1 meaning January 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/641515.rdf
Name: abundance
Units: cells/milliliter
Description: <p>Abundance of HLII or LLI clade Prochlorococcus cells containing the narB gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/641516.rdf
Name: temp
Units: degrees centigrade
Description: <p>Temperature at the sample location</p>
http://lod.bco-dmo.org/id/dataset-parameter/641517.rdf
Name: sal
Units: PSS-78
Description: <p>Salinity measured at the sample location</p>
http://lod.bco-dmo.org/id/dataset-parameter/641518.rdf
Name: depth
Units: meters
Description: <p>Depth at which the sample was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/641519.rdf
Name: sigma_0
Units: kilograms/cubic meter
Description: <p>Potential density</p>
http://lod.bco-dmo.org/id/dataset-parameter/641520.rdf
Name: standard_deviation
Units: cells/milliliter
Description: <p>Standard deviation of the abundance measurements</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
https://doi.org/10.1575/1912/bco-dmo.641735
download
onLine
dataset
<p>Sample processing and analyses are detailed in the publications listed below. Briefly, 100ml of seawater was collected onto 25mm dia polycarbonate filters (0.22um pore size), rinsed with Tris-buffered saline, flash frozen in liquid N2, and stored at -80C until extraction. DNA was extracted using a combination of 5min of bead beating and 15min heat lysis at 95C. Extracted DNA was used as template of quantitative PCR reactions using primers specifically designed to target the narB gene from the HLII and LLI clades of Prochlorococcus. Standard curves used for quantitation of field data were derived from DNA extracted from defined cell numbers of cultured representatives of each clade.</p>
Specified by the Principal Investigator(s)
<p>Estimated abundances that fell below the lowest value of the standard curve were set to the theoretical detection limit of 0.65 cells/mL. Samples were excluded if their melt curves contained multiple peaks or peaks different from those in the DNA standards. Samples were excluded if the coefficient of variation (standard deviation divided by the mean) was greater than 50%. The no data value "nd" refers to missing or excluded measurements.</p>
<p>Related files and references:</p>
<p>Analysis and data processing used the same field samples and methods as described in the following publication, but with different primer sets:
<br />
Malmstrom, R. R., Coe, A., Kettler, G. C., Martiny, A. C., Frias-Lopez, J., Zinser, E. R., & Chisholm, S. W. (2010). Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. The ISME Journal, 4(10), 1252–1264. doi:10.1038/ismej.2010.60</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
influx flow cytometer
influx flow cytometer
PI Supplied Instrument Name: influx flow cytometer PI Supplied Instrument Description:from Becton Dickinson, Franklin Lakes, NJ, USA Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Cruise: BATS_Prochlorococcus
BATS_Prochlorococcus
Bermuda Atlantic Time Series Vessel
vessel
BATS_Prochlorococcus
Sallie W. Chisholm
Massachusetts Institute of Technology
Cruise: HOT_Prochlorococcus
HOT_Prochlorococcus
Hawaii Ocean Time-series Vessel
vessel
HOT_Prochlorococcus
Sallie W. Chisholm
Massachusetts Institute of Technology
Bermuda Atlantic Time Series Vessel
vessel