http://lod.bco-dmo.org/id/dataset/3381
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
2010-11-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Five year time-series of Prochlorococcus ecotype abundance at HOT and BATS sites from 2002-2008 (C-MORE project, Prochlorococcus project)
2014-11-26
publication
2014-11-26
revision
BCO-DMO Linked Data URI
2014-11-26
creation
http://lod.bco-dmo.org/id/dataset/3381
Sallie W. Chisholm
principalInvestigator
Daniele Veneziano
Massachusetts Institute of Technology
principalInvestigator
Dr Rex Malmstrom
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. W., Chisholm, S. W., Chisholm, S. W., Veneziano, D., Malmstrom, R. (2014) Five year time-series of Prochlorococcus ecotype abundance at HOT and BATS sites from 2002-2008 (C-MORE project, Prochlorococcus project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2014-11-26 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3381 [access date]
Five year time series of Prochlorococcus ecotype abundance at HOT and BATS sites Dataset Description: <p>The goal was to collect long-term, high-resolution data on the temporal and spatial variability of Prochlorococcus ecotypes in the Pacific and Atlantic Oceans. The abundance of five Prochlorococcus ecotypes was determined by quantitative PCR at 12 depths every month for 5 years at two locations:</p>
<p>BATS location (5 nautical mile radius around 31 40'N, 64 10'W)<br />
HOT Station ALOHA (5 nautical mile radius around 22 45'N, 158 00' W)</p> Methods and Sampling: <p>Sample processing and analyses are detailed in the publication 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 different Prochlorococcus ecotypes. Standard curves used for quantitation of field data were derived from DNA extracted from cultured representatives belonging to each ecotype.</p>
<p>Malmstrom, RR, A Coe, GC Kettler, AC Martiny, J Frias-Lopez, ER Zinser, and SW Chisholm. 2010. Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. The ISME Journal. 4(10): 1252-1264</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0425602 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0425602
completed
Sallie W. Chisholm
(617) 253 1771
48-419 Department of Civil and Environmental Engineering 15 Vassar Street
Cambridge
MA
02139-4307
USA
chisholm@mit.edu
pointOfContact
Daniele Veneziano
Massachusetts Institute of Technology
77 Massachusetts Avenue
Cambridge
MA
02139
USA
venezian@mit.edu
pointOfContact
Dr Rex Malmstrom
Massachusetts Institute of Technology
925-927-2821
2800 Mitchell Dr.
Walnut Creek
CA
94598
USA
rrmalmstrom@lbl.gov
pointOfContact
asNeeded
Unknown
ecotype
site
lat
lon
year
month
day
abundance
temp
sal
depth
sigma_0
standard_deviation
date
yrday_gmt
cruiseid
theme
None, User defined
No BCO-DMO term
site
latitude
longitude
year
month_gmt
day_gmt
abundance
water temperature at measurement depth
salinity
depth
sigma-theta
date
day of year and decimal time (time zone GMT)
cruise id
featureType
BCO-DMO Standard Parameters
HOT_Prochlorococcus
BATS_Prochlorococcus
service
Deployment Activity
100 km north of Oahu, Hawaii
BATS at 31 40'N 64 10'W
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.
Center for Microbial Oceanography: Research and Education
http://cmore.soest.hawaii.edu/
Center for Microbial Oceanography: Research and Education
<h3>Project summary</h3>
<p>The <strong>Center for Microbial Oceanography: Research and Education</strong> (C-MORE) is a recently established (August 2006; NSF award: EF-0424599) NSF-sponsored Science and Technology Center designed to facilitate a more comprehensive understanding of the diverse assemblages of microorganisms in the sea, ranging from the genetic basis of marine microbial biogeochemistry including the metabolic regulation and environmental controls of gene expression, to the processes that underpin the fluxes of carbon, related bioelements and energy in the marine environment. Stated holistically, C-MORE's primary mission is: <em>Linking Genomes to Biomes</em>.</p>
<p>We believe that the time is right to address several major, long-standing questions in microbial oceanography. Recent advances in the application of molecular techniques have provided an unprecedented view of the structure, diversity and possible function of sea microbes. By combining these and other novel approaches with more well-established techniques in microbiology, oceanography and ecology, it may be possible to develop a meaningful predictive understanding of the ocean with respect to energy transduction, carbon sequestration, bioelement cycling and the probable response of marine ecosystems to global environmental variability and climate change. The strength of C-MORE resides in the synergy created by bringing together experts who traditionally have not worked together and this, in turn, will facilitate the creation and dissemination of new knowledge on the role of marine microbes in global habitability.</p>
<p>The new Center will design and conduct novel research, broker partnerships, increase diversity of human resources, implement education and outreach programs, and utilize comprehensive information about microbial life in the sea. The Center will bring together teams of scientists, educators and community members who otherwise do not have an opportunity to communicate, collaborate or design creative solutions to long-term ecosystem scale problems. The Center's research will be organized around four interconnected themes:</p>
<ul>
<li>(Theme I) microbial biodiversity,</li>
<li>(Theme II) metabolism and C-N-P-energy flow,</li>
<li>(Theme III) remote and continuous sensing and links to climate variability, and</li>
<li>(Theme IV) ecosystem modeling, simulation and prediction.</li>
</ul>
<p> Each theme will have a leader to help coordinate the research programs and to facilitate interactions among the other related themes. The education programs will focus on pre-college curriculum enhancements, in service teacher training and formal undergraduate/graduate and post-doctoral programs to prepare the next generation of microbial oceanographers. The Center will establish and maintain creative outreach programs to help diffuse the new knowledge gained into society at large including policymakers. The Center's activities will be dispersed among five partner institutions:</p>
<ul>
<li>Massachusetts Institute of Technology,</li>
<li>Woods Hole Oceanographic Institution,</li>
<li>Monterey Bay Aquarium Research Institute,</li>
<li>University of California at Santa Cruz and</li>
<li>Oregon State University</li>
</ul>
<p>and will be coordinated at the University of Hawaii at Manoa.</p>
<h4>Related Files:</h4>
<p><a href="http://bcodata.whoi.edu/C-MORE/C-MORE_SIP_ver_09-01-2008.pdf">Strategic plan (PDF file)</a></p>
C-MORE
largerWorkCitation
project
The Ecology of Prochlorococcus: Toward a Model System for Microbial Oceanography
https://osprey.bco-dmo.org/project/2128
The Ecology of Prochlorococcus: Toward a Model System for Microbial Oceanography
<p>The goal was to collect long-term, high-resolution data on the temporal and spatial variability of Prochlorococcus ecotypes in the Pacific and Atlantic Oceans. The abundance of five Prochlorococcus ecotypes was determined by quantitative PCR at 12 depths every month for 5 years at two locations.
</p>
<p>
The work was done in coordination with NSF-funded Bermuda Atlantic Time Series (BATS) and Hawaii Ocean Time-series (HOT), but not officially affiliated with these programs.
</p>
<p>
Geolocation:<br /><br />
BATS location (5 nautical mile radius around 31 40'N, 64 10'W)<br /><br />
HOT Station ALOHA (5 nautical mile radius around 22 45'N, 158 00' W)
</p>
<p>
References: <br /><br />
Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. Rex R Malmstrom, Allison Coe, Gregory C Kettler, Adam C Martiny, Jorge Frias-Lopez, Erik R Zinser, Sallie W Chisholm. The ISME Journal 4, 1252-1264 (13 May 2010) doi:10.1038/ismej.2010.60 <a href="http://www.nature.com/ismej/journal/v4/n10/full/ismej201060a.html" target="_blank">Link to paper</a>
</p>
<p>
Original Project Abstract:
</p>
<p>
The power of a model system for advancing our understanding of the natural world has been proven repeatedly in diverse sub-disciplines of science. This approach is equally valuable for the study of marine microbial ecology, either through the sustained study of a particular ecosystem, or through the study of a particular organism at all scales of organization from the genome to the ecosystem level. In this project the investigators will do the latter through a diverse set of laboratory and field studies designed to advance the understanding of Prochlorococcus, the numerically dominant phytoplankter in the world oceans. The objective is to understand what regulates the distribution and abundance of this important primary producer. Prochlorococcus has a number of features that make it a useful model organism for understanding the forces that shape marine microbial systems, and for generating hypotheses that will advance the field of Microbial Oceanography. It is the smallest and most abundant photosynthetic cell in the oceans, it can be isolated into culture, and it can be easily enumerated and studied in situ. Furthermore, it has the smallest genome of any known photosynthetic cell -- the minimal phototroph to date. Prochlorococcus is really a collection of "ecotypes", i.e., closely related but physiologically distinct populations that co-exist with different distributions along the light, temperature, nutrient, and predator (including viruses) gradients that shape their habitat. These distributions are determined by the relative fitness of the cells, i.e. the balance of growth rates and death rates along these gradients. The broad challenge is to understand the forces that have shaped this microdiversity over evolutionary time, and that guide the self-organization of these populations under different selective regimes. This is a multi-dimensional project designed to understand the "bottom up" (growth limitation by light, temperature, oxygen, and nutrients) and "top down" (mortality from viruses and grazing) influences on the population growth of different Prochlorococcus ecotypes through both laboratory and field studies. The project will involve high-throughput studies of the growth of ecotypes along gradients of environmental variables in the laboratory, as well as studies of the distribution of ecotypes along spatial and temporal gradients in the field (at the Hawaii and Bermuda Time Series Stations, along a longitudinal Atlantic transect, and in Oxygen Minimum Zones in the Arabian Sea and Peruvian Upwelling) using Q-PCR to assess their relative abundance. The investigators will also study the life cycle of viruses that infect Prochlorococcus and cross infect between ecotypes, and the growth and mortality rates of specific ecotypes in field samples due to grazing pressure. Another set of analyses will measure the full diversity of co-occurring Prochlorococcus in selected field samples, and work toward understanding at what level genetic diversity corresponds to ecologically meaningful diversity. Finally, the study will develop statistical methods for the characterization and analysis of Prochlorococcus ecotype "fitness spaces" established in the laboratory, and compare them with the distribution of ecotypes along environmental gradients in the field. This will allow a rigorously analysis of the degree to which different selective pressures shape the relative abundance of the different Prochlorococcus ecotypes in the oceans, and how they change over time and space.
</p>
Prochlorococcus
largerWorkCitation
project
eng; USA
biota
oceans
100 km north of Oahu, Hawaii; BATS at 31 40'N 64 10'W
2014-11-26
From projects that focused on the following 2 locations: 1. North Pacific Subtropical Gyre (large region around 22 45 N, 158 W) 2. BATS and HOT station ALOHA
0
BCO-DMO catalogue of parameters from Five year time-series of Prochlorococcus ecotype abundance at HOT and BATS sites from 2002-2008 (C-MORE project, Prochlorococcus 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/22646.rdf
Name: ecotype
Units: unknown
Description: <p>A group of organisms, normally a subdivision of a species, that is adapted to a specific environment</p>
http://lod.bco-dmo.org/id/dataset-parameter/22647.rdf
Name: site
Units: dimensionless
Description: <p>Location of the measurement, in this case one of two sites located at the HOT and BATS sites.</p>
http://lod.bco-dmo.org/id/dataset-parameter/22648.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude, north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/22649.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude, east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/22650.rdf
Name: year
Units: unknown
Description: <p>Year the measurement was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/22651.rdf
Name: month
Units: unknown
Description: <p>Month the measurement was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/22652.rdf
Name: day
Units: unknown
Description: <p>Day the measurement was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/22653.rdf
Name: abundance
Units: cells/milliliter
Description: <p>Number of bacteria counted</p>
http://lod.bco-dmo.org/id/dataset-parameter/22654.rdf
Name: temp
Units: degrees centigrade
Description: <p>Temperature at the sample location</p>
http://lod.bco-dmo.org/id/dataset-parameter/22655.rdf
Name: sal
Units: PSS-78
Description: <p>Salinity measured at the sample location</p>
http://lod.bco-dmo.org/id/dataset-parameter/22656.rdf
Name: depth
Units: meters
Description: <p>Depth at which the sample was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/22657.rdf
Name: sigma_0
Units: kilograms/cubic meter
Description: <p>Potential density</p>
http://lod.bco-dmo.org/id/dataset-parameter/22658.rdf
Name: standard_deviation
Units: cells/milliliter
Description: <p>Standard deviation of the abundance measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/22659.rdf
Name: date
Units: unknown
Description: <p>Date the sample was taken, in the form of mm/dd/yy</p>
http://lod.bco-dmo.org/id/dataset-parameter/22660.rdf
Name: yrday_gmt
Units: unknown
Description: <p>The year day the sample was taken, with 1 meaning January 1.</p>
http://lod.bco-dmo.org/id/dataset-parameter/22661.rdf
Name: cruiseid
Units: unknown
Description: <p>The cruise identification</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
768689
https://datadocs.bco-dmo.org/file/oAAmB5KIvvRJwK/hot_bats_2014.csv
hot_bats_2014.csv
Primary data file for dataset ID 3381
download
https://osprey.bco-dmo.org/dataset/3381/data/download
download
onLine
dataset
<p>Sample processing and analyses are detailed in the publication 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 different Prochlorococcus ecotypes. Standard curves used for quantitation of field data were derived from DNA extracted from cultured representatives belonging to each ecotype.</p>
<p>Malmstrom, RR, A Coe, GC Kettler, AC Martiny, J Frias-Lopez, ER Zinser, and SW Chisholm. 2010. Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. The ISME Journal. 4(10): 1252-1264</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. Missing data points were determined by linear interpolation when abundance estimates were available for the depths immediately above and below the missing value.</p>
<p>In November 2014, the online data were updated to correct relatively minor errors from HOT cruises 187 and 188. The "no data" value in the original data (-9999) was replaced with the "nd" string.</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
Cruise: HOT_Prochlorococcus
HOT_Prochlorococcus
Hawaii Ocean Time-series Vessel
vessel
HOT_Prochlorococcus
Sallie W. Chisholm
Massachusetts Institute of Technology
Cruise: BATS_Prochlorococcus
BATS_Prochlorococcus
Bermuda Atlantic Time Series Vessel
vessel
BATS_Prochlorococcus
Sallie W. Chisholm
Massachusetts Institute of Technology
Hawaii Ocean Time-series Vessel
vessel