Autonomous Underwater Vehicle Monterey Bay Time Series - CTD from AUV Makai on 2016-02-03

Data Type: Cruise Results
Version: 1
Version Date: 2023-08-15

» Center for Microbial Oceanography: Research and Education (C-MORE)
Scholin, ChrisMonterey Bay Aquarium Research Institute (MBARI)Principal Investigator
Ryan, John P.Monterey Bay Aquarium Research Institute (MBARI)Contact
Nahorniak, JasmineOregon 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

Autonomous Underwater Vehicle (AUV) Monterey Bay Time Series from Feb 2016. This data set includes CTD and fluorometer data from the Makai AUV, as context for ecogenomic sampling using an onboard Environmental Sample Processor (ESP).


Spatial Extent: N:36.8338 E:-121.828 S:36.7837 W:-121.888
Temporal Extent: 2016-02-03

Methods & Sampling

Data Processing Description

Original sensor data were bin averaged to 2-second resolution.


BCO-DMO Processing Description

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

[ table of contents | back to top ]

Data Files

AUV Monteray Bay CTD
filename: 644012_v1_auv_monteray_bay_ctd.csv
(Comma Separated Values (.csv), 2.80 MB)
Primary data file for dataset ID 644012, version 1

[ table of contents | back to top ]


ISO_DateTime_UTCDate and time (UTC) formatted to ISO 8601 standard unitless
latlatitude (north is positive) decimal degrees
lonlongitude (east is positive) decimal degrees
depthdepth sample meters
tempTemperature from CTD degrees Celsius
salSalinity from CTD dimensionless
chl_a_fluorchlorophyll-a fluorometric method micrograms/liter

[ table of contents | back to top ]


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|

[ table of contents | back to top ]



AUV Makai
Start Date
End Date

[ table of contents | back to top ]

Project Information

Center for Microbial Oceanography: Research and Education (C-MORE)

Coverage: North Pacific Subtropical Gyre (large region around 22 45 N, 158 W)

Project summary

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:

  • (Theme I) microbial biodiversity,
  • (Theme II) metabolism and C-N-P-energy flow,
  • (Theme III) remote and continuous sensing and links to climate variability, and
  • (Theme IV) ecosystem modeling, simulation and prediction.

  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:

  • Massachusetts Institute of Technology,
  • Woods Hole Oceanographic Institution,
  • Monterey Bay Aquarium Research Institute,
  • University of California at Santa Cruz and
  • Oregon State University

and will be coordinated at the University of Hawaii at Manoa.

Related Files:

Strategic plan (PDF file)

[ table of contents | back to top ]


Funding SourceAward
NSF Division of Biological Infrastructure (NSF DBI)
David and Lucile Packard Foundation (Packard)

[ table of contents | back to top ]