The advent of ocean observatories is creating unique opportunities for deploying novel sensor systems. We are exploring that potential through the development and application of the Environmental Sample Processor (ESP). ESP is an electromechanical/fluidic system designed to collect discrete water samples, concentrate microorganisms, and automate application of molecular probe technologies. Development and application of ESP grew from extensive partnerships galvanized by the National Oceanographic Partnership Program. Near-real-time observations are currently achieved using low-density DNA probe and protein arrays. Filter-based sandwich hybridization methodology enables direct detection of ribosomal RNA sequences diagnostic for groups of bacteria and archaea, as well as a variety of invertebrates and harmful algal species. An antibody-based technique is used for detecting domoic acid, an algal biotoxin. To date, ESP has been deployed in ocean waters from the near surface to 1000 m. Shallow-water deployments demonstrated application of all four types of assays in single deployments lasting up to 30 days and provided the first remote detection of such phylogenetically diverse organisms and metabolites on one platform. Deep-water applications focused on detection of invertebrates associated with whale falls, using remotely operated vehicle-based operations lasting several days. Current work emphasizes incorporating a four-channel, real-time polymerase chain reaction module, extending operations to 4000-m water depth, and increasing deployment duration.
View Issue TOC
Volume 22, No. 2
Pages 158 - 167
Remote Detection of Marine Microbes, Small Invertebrates, Harmful Algae, and Biotoxins using the Environmental Sample Processor (ESP)
Christopher Scholin , Gregory Doucette, Scott Jensen, Brent Roman , Douglas Pargett , Roman Marin III , Christina Preston, William Jones, Jason Feldman, Cheri Everlove , Cheri Everlove , Nilo Alvarado, Eugene Massion, James Birch , Dianne Greenfield, Robert Vrijenhoek, Christina Mikulski , Kelly Jones
Scholin, C., G. Doucette, S. Jensen, B. Roman, D. Pargett, R. Marin III, C. Preston, W. Jones, J. Feldman, C. Everlove, A. Harris, N. Alvarado, E. Massion, J. Birch, D. Greenfield, R. Vrijenhoek, C. Mikulski, and K. Jones. 2009. Remote detection of marine microbes, small invertebrates, harmful algae, and biotoxins using the Environmental Sample Processor (ESP). Oceanography 22(2):158–167, https://doi.org/10.5670/oceanog.2009.46.
Ahn, S., D.M. Kulis, D.L. Erdner, D.M. Anderson, and D.R. Walt. 2006. Fiber-optic microarray for simultaneous detection of multiple harmful algal bloom species. Applied and Environmental Microbiology 72:5,742–5,749.
Belgrader, P., C.J. Elkin, S.B. Brown, S.N. Nasarabadi, R.G. Langlois, F.P. Milanovich, B.W. Colston Jr., and G.D. Marshall. 2003. A reusable flow-through polymerase chain reaction instrument for the continuous monitoring of infectious biological agents. Analytical Chemistry 75:3,446–3,450.
Doucette, G.J., C.M. Mikulski, K.L. Jones, K.L. King, D.I. Greenfield, R. Marin III, S. Jensen, B. Roman, C.T. Elliott, and C.A. Scholin. In press. Remote, subsurface detection of the algal toxin domoic acid onboard the Environmental Sample Processor: Assay development and field trials. Harmful Algae.
Ellison, C.K., and R.S. Burton. 2005. Application of bead array technology to community dynamics of marine phytoplankton. Marine Ecology Progress Series 288:75–85.
ESP Technology. 2008. Illustrations showing SHA and cELISA techniques. Available online at: http://www.mbari.org/ESP/esp_technology.htm (accessed April 6, 2009).
ESP Works. 2008. Animation showing operation of the ESP in surface waters. Available online at: http://www.mbari.org/ESP/espworks.htm (accessed April 6, 2009).
Frias-Lopez, J., Y. Shi, G.W. Tyson, M.L. Coleman, S.C. Schuster, S.W. Chisholm, and E.F. DeLong. 2008. Microbial community gene expression in ocean surface waters. Proceedings of the National Academy of Sciences of the United States of America 105:3,805–3,810.
GEOHAB. 2008. Global Ecology and Oceanography of Harmful Algal Blooms. Available online at: http://www.geohab.info/(accessed April 10, 2009).
Goffredi, S.K., W. Jones, C. Scholin, R. Marin, S. Hallam, and R.C. Vrijenhoek. 2006. Molecular detection of marine larvae. Marine Biotechnology 8:149–160, https://doi.org/10.1007/s10126-005-5016-2.
Goffredi, S.K., R. Wilpiszeski, R. Lee, and V.J. Orphan. 2008. Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California. The ISME Journal 2:204–220.
Goodwin, K.D., and R.W. Litaker. 2008. Emerging technologies for monitoring recreational waters for bacteria and viruses. Pp. 381–404 in Oceans and Human Health: Risks and Remedies from the Seas. P.J. Walsh, S.L. Smith, L.E. Fleming, H.M. Solo-Gabriele, and W.H. Gerwick, eds, Academic Press, London.
Greenfield, D.I., R. Marin III, S. Jensen, E. Massion, B. Roman, J. Feldman, and 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.
Haywood, A.J., C.A. Scholin, R. Marin III, K. Petrik, R. Pigg, M. Garrett, K.A. Steidinger, and C. Heil. 2009. Detection of Karenia brevis in Florida coastal waters using sandwich hybridization assays in two formats. Pp 95-100 in Proceedings of the 6th International Conference on Molluscan Shellfish Safety. Royal Society of New Zealand Miscellaneous Series 71, Blenheim, Marlborough, New Zealand, 355 pp.
Huber, J.A., D.B. Welch, H.G. Morrison, S.M. Huse, P.R. Neal, D.A. Butterfield, and M.L. Sogin. 2007. Microbial population structures in the deep marine biosphere. Science 318:97–100.
Jones, W.J., C. Preston, R. Marin III, C. Scholin, and R. Vrijenhoek. 2008. A robotic molecular method for in situ detection of marine invertebrate larvae. Molecular Ecology Resources 8:540–550.
Kvitek, R.G, J.D. Goldberg, G.J. Smith, G.J. Doucette, and M.W. Silver. 2008. Domoic acid contamination within eight representative species from the benthic food web of Monterey Bay, California, USA. Marine Ecology Progress Series 367:35–47.
Landsberg, J., F. Van Dolah, and G. Doucette. 2005. Marine and estuarine harmful algal blooms: Impacts on human and animal health. Pp. 165–215 in Oceans and Health: Pathogens in the Marine Environment. S. Belkin and R.R. Colwell, eds, Springer, New York.
Lefebvre, K.A., S. Bargu, T. Kieckhefer, and M.W. Silver. 2002. From sanddabs to blue whales: The pervasiveness of domoic acid. Toxicon 40:971–977.
Mariella, R., Jr. 2008. Sample preparation: The weak link in microfluidics-based biodetection. Biomed Microdevices, https://doi.org/10.1007/s10544-008-9190-7.
NEPTUNE. 2008. Ecogenomics. Available online at: http://www.neptune.washington.edu/research/index.jsp?keywords=ECOGNM&title=Ecogenomics; see also http://www.neptune.washington.edu/about/index.jsp?keywords=NEWRDS&title=New%20Era%20of%20Discovery (accessed April 6, 2009).
ORION. 2008. Ocean Research Interactive Observing Networks. Available online at: http://www.orionprogram.org/documents/default.html (accessed April 6, 2009).
Palmer, C.J., J.A. Bonilla, T.D. Bonilla, K.D. Goodwin, S.M. Elmir, A.M. Abdelzaher, and H.M. Solo-Gabriele. 2008. Future of microbial ocean water quality monitoring. Pp. 405–421 in Oceans and Human Health: Risks and Remedies from the Seas. P.J. Walsh, S.L. Smith, L.E. Fleming, H.M. Solo-Gabriele, and W.H. Gerwick, eds, Academic Press, London.
Paul, J., C. Scholin, G. van den Engh, and M.J. Perry. 2007. In situ instrumentation. Oceanography 20(2):70–78. Available online at: http://www.tos.org/oceanography/issues/issue_archive/20_2.html (accessed April 6, 2009).
Preston, C., R. Marin III, S. Jenson, J. Feldman, E. Massion, E. DeLong, M. Suzuki, K. Wheeler, D. Cline, N. Alvarado, and C. Scholin. 2009. Near real-time, autonomous detection of marine bacterioplankton on a coastal mooring in Monterey Bay, California, using rRNA-targeted DNA probes. Environmental Microbiology 11:1,168–1,180, https://doi.org/10.1111/j.1462-2920.2009.01848.x.
Ramsdell, J.S. 2007. The molecular and integrative basis to domoic acid toxicity. Pp. 223–250 in Phycotoxins: Chemistry and Biochemistry. L. Botana, ed., Blackwell Publishing Professional, Cambridge.
Ramsdell, J.S., and T.S. Zabka. 2008. In utero domoic acid toxicity: A fetal basis to adult disease in the California Sea Lion (Zalophus californianus). Marine Drugs 6:262–290.
Ramsdell, J.S., D.M. Anderson, and P.M. Glibert. eds. 2005. Harmful Algal Research and Response: A National Environmental Science Strategy 2005–2015. Ecological Society of America, Washington, DC, 96 pp.
Rich, V.I., K. Konstantinidis, and E.F. DeLong. 2007. Design and testing of ‘genome-proxy’ microarrays to profile marine microbial communities. Environmental Microbiology 10:506–521.
Roman, B., C. Scholin, S. Jensen, E. Massion, R. Marin III, C. Preston, D. Greenfield, W. Jones, and K. Wheeler. 2007. Controlling a robotic marine water sampler with the Ruby scripting language. Journal of American Laboratory Automation 12:56–61.
Sandifer, P., C. Sotka, D. Garrison, and V. Fay, eds. 2007. Interagency Oceans and Human Health Research Implementation Plan: A Prescription for the Future. Interagency Working Group on Harmful Algal Blooms, Hypoxia, and Human Health of the Joint Subcommittee on Ocean Science and Technology. Washington, DC, 92 pp.
Scholin, C. 2009. What are “ecogenomic sensors?” A review and thoughts for the future. Ocean Science Discussions 6:191–213.
Scholin, C.A., G.J. Doucette, and A.D. Cembella. 2008. Prospects for developing automated systems for in situ detection of harmful algae and their toxins. Pp. 413–462 in Real-Time Coastal Observing Systems for Ecosystem Dynamics and Harmful Algal Blooms. M. Babin, C.S. Roesler, and J.J. Cullen, eds, UNESCO Publishing, Paris, France.
Scholin, C., S. Jensen, B. Roman, E. Massion, R. Marin III, C. Preston, D. Greenfield, W. Jones, and K. Wheeler. 2006. The Environmental Sample Processor (ESP): An autonomous robotic device for detecting microorganisms remotely using molecular probe technology. Paper presented at OCEANS 2006 MTS/IEEE Conference, Boston, MA, September 18–21, 2006. Marine Technology Society, Columbia, MD.
This is an open access article made available under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution, and reproduction in any medium or format as long as users cite the materials appropriately, provide a link to the Creative Commons license, and indicate the changes that were made to the original content. Images, animations, videos, or other third-party material used in articles are included in the Creative Commons license unless indicated otherwise in a credit line to the material. If the material is not included in the article’s Creative Commons license, users will need to obtain permission directly from the license holder to reproduce the material.