http://lod.bco-dmo.org/id/dataset/555991
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
2015-04-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Diel metatranscriptome study in Monterey Bay, California, USA from August to September 2012 (C-MORE project, CANON project)
2015-04-16
publication
2015-04-16
revision
BCO-DMO Linked Data URI
2015-04-16
creation
http://lod.bco-dmo.org/id/dataset/555991
Edward DeLong
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: DeLong, E. (2015) Diel metatranscriptome study in Monterey Bay, California, USA from August to September 2012 (C-MORE project, CANON project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 16 April 2015) Version Date 2015-04-16 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/555991 [access date]
Diel_Metatrans Dataset Description: <p>Diel metatranscriptome study in Monterey Bay, 2012.</p>
<p>Data from the accession numbers listed below can be accessed from NCBI (http://www.ncbi.nlm.nih.gov/).</p>
<p><strong>GenBank accession numbers </strong><br />
<strong>BioProject</strong>: PRJNA268385 (http://www.ncbi.nlm.nih.gov/bioproject/PRJNA268385)<br />
<strong>SRP</strong>: SRP050269 (http://www.ncbi.nlm.nih.gov/sra/?term=SRP050269)</p> Methods and Sampling:
Funding provided by US Department of Energy (DOE) Award Number: unknown C-MORE DOE
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 Gordon and Betty Moore Foundation (GBMF) Award Number: unknown C-MORE Moore
completed
Edward DeLong
Massachusetts Institute of Technology
CMORE 114
Honolulu
HI
96822
USA
edelong@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 16 April 2015
Unknown
lat
lon
sample
depth
date
BioProject
SRX
BioSample
Environmental Sample Processor (ESP)
theme
None, User defined
latitude
longitude
sample identification
depth
date
accession number
featureType
BCO-DMO Standard Parameters
Environmental Sample Processor
instrument
BCO-DMO Standard Instruments
CANON_2012_ESP
service
Deployment Activity
Coastal California, USA
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
Controlled, Agile, and Novel Observing Network
http://www.mbari.org/canon/
Controlled, Agile, and Novel Observing Network
<p>Growth and death of microorganisms in the sea occur as ephemeral features that continually evolve and interact with the environment. These “booms and busts” reflect the interplay between physics, chemistry, and biology, and represent the core of the oceanic food web. But not all of this activity is benign. Some blooms can be harmful to humans and wildlife, and can bring negative economic consequences. The ability to achieve mechanistic understanding of these phenomena has eluded us because of technical difficulties tracking water masses and the rapidly changing life they carry. The Controlled, Agile, and Novel Observing Network (CANON) team aims to overcome that limitation by creating new ways to remotely assess oceanic conditions and collect samples of microorganisms for in situ analysis as well as for return to shoreside laboratories.</p>
<p>How does the pelagic food web respond to changes in the natural environment? Our ability to answer this question is central to predicting how the oceans will respond to human perturbations such as increasing atmospheric carbon dioxide (CO2) levels, nutrient runoff from agricultural and aquacultural activities, dispersal of various pollutants, and climate change. Yet present-day models are not capable of accurately predicting future consequences because very basic questions about the food web are still unanswered. Further, unexpected but significant events will continue to appear requiring an observing system capable of rapidly responding to these new challenges as well as investigating the basic processes required for accurate environmental prediction.</p>
<p>The food web of interest is much more complex than it might initially appear. Take the marine microorganisms at its core—not composed of one entity, but rather they span a tremendous range of physiological capabilities and mediate many different biogeochemical processes as functionally diverse as that of the full biota on land. Thus, changes such as increased atmospheric CO2 levels, which will reduce ocean pH, will have different consequences for the many organisms in the marine environment, and these in turn will propagate through the food web. While the last decade has seen a revolution in understanding of the diversity and importance of microbial populations in the ocean, our understanding of how those populations respond to changes in their environment—and to other microbes—is rudimentary at best. Developing a better understanding of microbial dynamics through the development of new ocean observation capabilities is the initial thrust of the CANON program.</p>
<p> </p>
<p>A key initial premise of CANON is to provide a new class of observation systems that will be able to follow and facilitate the study of organism assemblages and the transitions they undergo in the ocean environment. This is a critical development. The spatial and temporal sampling resolutions currently possible are not relevant to the spatial and temporal scales on which microbial processes occur. A fundamental principle for the initiative is that processes and microbes must be studied at scales relevant to the organisms’ adaptive strategies to determine how metabolism influences larger-scale ecosystem dynamics. The initiative builds on lessons learned from previous multi-platform, multi-institutional field programs of the <a class="western" href="http://www.mbari.org/canon/AOSNdefault.htm">Autonomous Ocean Sampling Network (AOSN)</a>. In contrast to the earlier field programs, which addressed observing and predicting the physical ocean, the AOSN team is further developing the Collaborative Ocean Observatory Portal and other tools and methods to observe marine microorganism populations.</p>
<p>The CANON team aims to merge observation, modeling, and prediction to cast projections of biological, chemical, and physical gradients within a defined region. By directing small fleets of mobile sensors within that domain, they will detect specific phenomena remotely, collect physical samples of microbes, algae, and small invertebrates autonomously, and track the evolution of biological patches over time. The system in its final form will be able to provide scientists and managers with the information required to interpret the mechanisms detected and make decisions as to how to proceed.</p>
<p>CANON will bring the biological insights to the requirements of new sensor development, based on cutting-edge approaches to genomics, transcriptomics, and physiology studies, and the technological innovations necessary to access the environment in unprecedented resolution, letting environmental conditions guide sampling decisions in real time and in situ.</p>
CANON
largerWorkCitation
project
eng; USA
biota
oceans
Coastal California, USA
2015-04-16
From projects that focused on the following 2 locations: 1. North Pacific Subtropical Gyre (large region around 22 45 N, 158 W) 2. Coastal California, USA
0
BCO-DMO catalogue of parameters from Diel metatranscriptome study in Monterey Bay, California, USA from August to September 2012 (C-MORE project, CANON 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/556001.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude (positive north)</p>
http://lod.bco-dmo.org/id/dataset-parameter/556002.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude (positive east)</p>
http://lod.bco-dmo.org/id/dataset-parameter/556003.rdf
Name: sample
Units: dimensionless
Description: <p>sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/556004.rdf
Name: depth
Units: meters
Description: <p>depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/556005.rdf
Name: date
Units: YYYYMMDD
Description: <p>date</p>
http://lod.bco-dmo.org/id/dataset-parameter/556006.rdf
Name: BioProject
Units: dimensionless
Description: <p>NCBI BioProject accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/556007.rdf
Name: SRX
Units: dimensionless
Description: <p>NCBI SRX accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/556008.rdf
Name: BioSample
Units: dimensionless
Description: <p>NCBI BioSample accession number</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
9522
https://datadocs.bco-dmo.org/file/GwwAkDMfBg87Jz/diel_metatrans.csv
diel_metatrans.csv
Primary data file for dataset ID 555991
download
https://osprey.bco-dmo.org/dataset/555991/data/download
download
onLine
dataset
<p># C-MORE Monterey Bay diel metatranscriptome study<br />
# DeLong Lab - Massachusetts Institute of Technology<br />
# Ed DeLong<br />
# CMORE/MontereyBay<br />
# Date ingested into BCO-DMO: April 16 2015</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
Environmental Sample Processor (ESP)
Environmental Sample Processor (ESP)
PI Supplied Instrument Name: Environmental Sample Processor (ESP) PI Supplied Instrument Description:Environmental Sample Processor (ESP) Instrument Name: Environmental Sample Processor Instrument Short Name:ESP Instrument Description: The MBARI Environmental Sample Processor—the ESP—provides on-site (in situ) collection and analysis of water samples from the subsurface ocean. The instrument is an electromechanical/fluidic system designed to collect discrete water samples, concentrate microorganisms or particles, and automate application of molecular probes and qPCR which identify microorganisms and their gene products. The ESP also archives samples so that further analyses may be done after the instrument is recovered.
Environmental Sample Processor
See references below for methodology used on the ESP:
Greenfield, D.I., R. Marin III, S. Jensen, E. Massion, B. Roman, J. Feldman, C. Scholin (2006). Application of the Environmental Sample Processor (ESP) methodology for quantifying Pseudo-nitzschia australis using ribosomal RNA-targeted probes in sandwich and fluorescent in situ hybridization. Limnology and Oceanography: Methods 4: 426-435.
Greenfield, D., R. Marin III, G.J. Doucette, C. Mikulski, S. Jensen, B. Roman, N. Alvarado, and C.A. Scholin (2008). Field applications of the second-generation Environmental Sample Processor (ESP) for remote detection of harmful algae: 2006-2007. Limnology and Oceanography: Methods 6: 667-679.
Marin III, R., and C. Scholin (2010). Sandwich Hybridization. In: Microscopic and molecular methods for quantitative phytoplankton analysis (Chapter 12), edited by B. Karlson, C. Cusack, and E. Bresnan, E.. IOC Manuals and Guides, no. 55. (IOC/2010/MG/55) Paris, UNESCO. 110 pp.
Ottesen, E.A., R. Marin III, C.M. Preston, C.R. Young, J.P. Ryan, C.A. Scholin, and E.F. DeLong (2011). Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. The ISME Journal, 5: 1881-1895, doi: 10.1038/ismej.2011.70.
Ottesen, E.A., C.R. Young, J.M. Eppley, J.P. Ryan, F.P. Chavez, C.A. Scholin, and E.F. DeLong (2013). Pattern and synchrony of gene expression among sympatric marine microbial populations. Proceedings of the National Academy of Sciences, 110: E488-E497, doi: 10.1073/pnas.1222099110.
Ottesen, E.A., C.M. Young, S.M. Gifford, J.M. Eppley, R. Marin III, S.C. Schuster, C.A. Scholin, and E.F. DeLong (2014). Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science, 345: 207-212, 10.1126/science.1252476.
Preston, C.M., A. Harris, J.P. Ryan, B. Roman, R. Marin III, S. Jensen, C. Everlove, J. Birch, J.M. Dzenitis, D. Pargett, M. Adachi, K. Turk, J.P. Zehr, and C.A. Scholin (2011). Underwater application of quantitative PCR on an ocean mooring. PLoS ONE, 6:e22522, doi: 10.1371/journal.pone.0022522.
Robidart, J.C., C.M. Preston, R.W. Paerl, K.A. Turk, A.C. Mosier, C.A. Francis, C.A. Scholin, and J.P. Zehr (2011). Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation. The ISME Journal, 6: 513-523, doi: 10.1038/ismej.2011.127.
Robidart, J., M.J. Church, J.P. Ryan, F. Ascani, S.T. Wilson, D. Bombar, R. Marin III, K.J. Richards, D.M. Karl, C.A. Scholin, and J.P Zehr (2014). Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean. The ISME Journal, 8: 1175-1185, 10.1038/ismej.2013.244.
Saito, M.A., V.V. Bulygin, D.M. Moran, C. Taylor, and C. Scholin (2011). Examination of microbial proteome preservation techniques applicable to autonomous environmental sample collection. Frontiers in Aquatic Microbiology, 2: doi: 10.3389/fmicb.2011.00215.
Scholin, C.. (2010). What are “ecogenomic sensors?” A review and thoughts for the future. Ocean Science 6: 51-60.
Ussler III, W., C.M. Preston, P. Tavormina, D. Pargett, S. Jensen, B. Roman, R. Marin III, S.R. Shah, P.R. Girguis, J.M. Birch, V.J. Orphan, and C. Scholin (2013). Autonomous application of quantitative PCR in the deep sea: In situ surveys of aerobic methanotrophs using the deep-sea Environmental Sample Processor. Environmental Science and Technology, 47: 9339–9346, doi: 10.1021/es4023199.
Varaljay, V.A, J. Robidart, C.M. Preston, S.M. Gifford, B. Durham, A.S. Burns, J.P. Ryan, R. Marin III, R.P. Kiene, J.P Zehr, C.A. Scholin, M. Moran. 2015. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate. ISME Journal, doi:10.1038/ismej.2015.23|
Deployment: CANON_2012_ESP
CANON_2012_ESP
Environmental Sample Processor
float
CANON_2012_ESP
Dr Chris Scholin
Monterey Bay Aquarium Research Institute
Environmental Sample Processor
float