| Contributors | Affiliation | Role |
|---|---|---|
| Scholin, Chris | Monterey Bay Aquarium Research Institute (MBARI) | Principal Investigator |
| Ryan, John P. | Monterey Bay Aquarium Research Institute (MBARI) | Contact |
| Nahorniak, Jasmine | Oregon State University (OSU-CEOAS) | Data Manager |
| Gegg, Stephen R. | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
| Merchant, Lynne M. | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
Original sensor data were bin averaged to 2-second resolution.
The date and time columns in the submitted file were combined to create an ISO datetime column named ISO_DateTime_UTC and of format YYYY-MM-DDThh:mm:ssZ
| File |
|---|
AUV Monteray Bay CTD filename: 644012_v1_auv_monteray_bay_ctd.csv (Comma Separated Values (.csv), 2.80 MB) MD5:5885af1113684d9f2a739c4ae15de9a6 Primary data file for dataset ID 644012, version 1 |
| Parameter | Description | Units |
| ISO_DateTime_UTC | Date and time (UTC) formatted to ISO 8601 standard | unitless |
| lat | latitude (north is positive) | decimal degrees |
| lon | longitude (east is positive) | decimal degrees |
| depth | depth sample | meters |
| temp | Temperature from CTD | degrees Celsius |
| sal | Salinity from CTD | dimensionless |
| chl_a_fluor | chlorophyll-a fluorometric method | micrograms/liter |
| Dataset-specific Instrument Name | Makai AUV |
| Generic Instrument Name | Autonomous Underwater Vehicle |
| Generic Instrument Description | An Autonomous Underwater Vehicle (AUV) is a free-roving platform operating in the water column with propulsion but no human operator on board (e.g. Autosub, Gavia). |
| Dataset-specific Instrument Name | Environmental Sample Processor |
| Generic Instrument Name | Environmental Sample Processor |
| Generic 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| |
| Website | |
| Platform | AUV Makai |
| Start Date | 2015-07-22 |
| End Date | 2099-01-01 |
| Description |
The Center for Microbial Oceanography: Research and Education (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: Linking Genomes to Biomes.
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.
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:
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:
and will be coordinated at the University of Hawaii at Manoa.
| Funding Source | Award |
|---|---|
| NSF Division of Biological Infrastructure (NSF DBI) | |
| David and Lucile Packard Foundation (Packard) |