Environmental Sample Processor (ESP) publications

Sepulveda AJ, Hoegh A, Gage JA, Caldwell Eldridge SL, Birch JM, Stratton C, Hutchins PR and Barnhart EP. 2021. Integrating environmental DNA results with diverse data sets to improve biosurveillance of river health. Front. Ecol. Evol. 9:620715. doi: https://doi.org/10.3389/fevo.2021.620715

Moore, S.K, J.B. Mickett, G.J. Doucette, N.G. Adams, C.M. Mikulski, J.M. Birch, B. Roman, N. Michel-Hart, J.A. Newton. 2021. An autonomous platform for near real-time surveillance of harmful algae and their toxins in dynamic coastal shelf environments. Accepted in J. of Marine Science and Engineering.

Zhang, Y., J. P. Ryan, B.W. Hobson, B. Kieft, A. Romano, B. Barone, C.M. Preston, B. Roman, B. Raanan, D. Pargett, M. Dugenne, A.E. White, F.H. Freitas, S. Poulos, S.T. Wilson, E.F. DeLong, D.M. Karl, J.M. Birch, J.G. Bellingham, and C.A. Scholin. 2021. A system of coordinated autonomous robots for Lagrangian studies of microbes in the oceanic deep chlorophyll maximum. Science Robotics 6, eabb9138.

Sepulveda, A.J., J.M. Birch, E.P. Barnhart, C.M. Merkes, K.M. Yamahara, R. Marin III, S.M. Kinsey, P.R. Wright, C. Schmidt. 2020. Robotic environmental DNA bio-surveillance of freshwater health. Scientific Reports 10:14389. https://doi.org/10.1038/s41598-020-71304-3.

Cunha, M., L. Génio, F. Pradillon, M.C. Henry, S. Beaulieu, J. Birch, F. Campuzano, M. Carretón, F. De Leo, J. Gula, S. Laming, D. Lindsay, F. Matos, A. Metaxas, K. Meyer-Kaiser, S. Mills, H. Queiroga, C. Rodrigues, J. Sarrazin, H. Watanabe, R. Young, C. Young. 2020. Foresight Workshop on Advances in Ocean Biological Observations: a sustained system for deep-ocean meroplankton. Research Ideas and Outcomes 6: e54284 https://doi.org/10.3897/rio.6.e54284

Zhang, Y., B. Kieft, B. Hobson, B. Ranaan, S. Urmy, K. Pitz, C. Preston, B. Roman, K. Benoit-Bird, J. Birch, F. Chavez, C. Scholin. 2020. Persistent Sampling of vertically migrating biological layers by an autonomous underwater vehicle within the beam of a seabed-mounted echosounder. IEEE J. of Oceanic Engineering. https://doi: 10.1109/JOE.2020.2982811

Evans, S. J. Birch, J. Breier Jr, M. Jakuba, M. Saito, and J. Robidart. 2019. Ocean robots uncover microbial secrets. Microbiology Today pp 18-21., Feb 2019.

Zhang, Y., J. Ryan, B. Kieft, B. Hobson, R. McEwen, M. Godin, J. Harvey, B. Benedetto, J. Bellingham, J. Birch, C. Scholin, F. Chavez. 2019. Targeted Sampling by Autonomous Underwater Vehicles. Frontiers in Marine Science, 6:415. https://DOI.org/10.3389/fmars.2019.00415.

Nowinski, B., J. Motard-Côté, M. Landa, C. Preston, C. Scholin, J. Birch, R. Keine, M. Moran. 2019. Microdiversity and Temporal Dynamics of Bacterial Dimethylsulfoniopropionate Genes. Environmental Microbiology 21 (5):1687-1701. DOI: https://doi.org/10.1111/1462-2920.14560

Zhang, B. Kieft, B. W. Hobson, J. Ryan, B. Barone, C. Preston, B. Roman, B-Y. Raanan, R. Marin III, T. O’Reilly, C. Rueda, D. Pargett, K. Yamahara, S. Poulos, A. Romano, G. Foreman, H. Ramm, S. Wilson, E. DeLong, D. Karl, J. Birch, J. Bellingham, and C. Scholin. 2019. “Autonomous Tracking and Sampling of the Deep Chlorophyll Maximum Layer in an Open-Ocean Eddy by a Long Range Autonomous Underwater Vehicle,” IEEE Journal of Oceanic Engineering, 45(4) pp 1308-1321. DOI: https://doi.org/10.1109/JOE.2019.2920217

Kiene, R., B. Nowinski, K. Esson, C. Preston, R. Marin III, J. Birch, C. Scholin, J. Ryan, M. Moran. 2019. Unprecedented DMSP concentrations in a massive dinoflagellate bloom in Monterey Bay, CA. Geophysical Research Letters, 46 (21):12279-12288 https://doi.org/10.1029/2019GL085496

Yamahara, K., C. Preston, J. Birch, K. Walz, R. Marin III, S. Jensen, D. Pargett, B. Roman, Y. Zhang, J. Ryan, W. Ussler, B. Hobson, B. Kieft, B. Raanan, K. Goodwin, F. Chavez, and C. Scholin. 2019. In-situ autonomous acquisition and preservation of marine environmental DNA using an autonomous underwater vehicle. Frontiers in Marine Science, 6:373. https://doi.org/10.3389/fmars.2019.00373

Krolicka, A., Boccadoro, C., Mæland Nilsen, M., Demir-Hilton, E., Birch, J., Preston, C., Scholin, C., Baussant, T. 2019. Identification of microbial key-indicators of oil contamination at sea through tracking of oil biotransformation: An Arctic field and laboratory study. Sci Total Environ 696:133715. doi: https://doi.org/10.1016/j.scitotenv.2019.133715.

Nowinski, B., C. Smith, C. Thomas, K. Esson, R. Marin III, C. Preston, J. Birch, C. Scholin, M. Huntemann, A. Clum, B. Foster, B. Foster, S. Roux, K. Palaniappan, N. Varghese, S. Mukherjee, T. Reddy, C. Daum, A. Copeland, I. Chen, N. Ivanova, N. Kyrpides, T. Glavina del Rio, W. Whitman, R. Kiene, E. Eloe-Fadrosh, and M. Moran. 2019. Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom. Nature: Scientific data. https://doi.org/10.1038/s41597-019-0132-4.

Kolody, B., McCrow, J. P., Zeigler Allen, L., Aylward, F.O., Fontanez, K. M., A., Moustafa, A., Moniruzzaman, M., Chavez, F.P., Scholin, C.A, Allen, E. E., Worden, A. Z., Delong, E. F., Allen, A. E. 2019 (2019). Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. ISME J 13, 2817–2833

Brett W. Hobson, Brian Kieft, Ben Raanan, Yanwu Zhang, James Birch, John P. Ryan, Francisco P. Chavez. 2018. An Autonomous Vehicle-Based Open Ocean Lagrangian Observatory. IEEE AUV2018 Proceedings. Porto, Portugal.

Birch, J. B. Barone, E. DeLong, G. Foreman, K. Gomes, B. Hobson, S. Jensen, D. Karl, B. Kieft, R. Marin III, T. O’Reilly, D. Pargett, S. Poulos, C. Preston, H. Ramm, B. Roman, A. Romano, J. Ryan, C. Scholin, W. Ussler, S. Wilson, K. Yamahara, Y. Zhang. 2018. Autonomous Targeted Sampling of the Deep Chlorophyll maximum layer in a subtropical north Pacific eddy. Proceedings IEEE Oceans, Charleston, SC Oct 22-25, 2018. https://doi.org/10.1109/OCEANS.2018.8604898

Birch, J. 2018. Collecting and processing samples in remote and dangerous places: the Environmental Sample Processor as a case study. Pure and Applied Chemistry 90 (10): 1625-1630. https://doi.org/10.1515/pac-2018-0201

Scholin, C., Birch,J., Jensen, S., Marin III, R., Massion, E., Pargett, D., Preston, C., Roman, B., Ussler III, W. 2018. The quest to develop ecogenomic sensors: A 25-year history of the Environmental Sample Processor (ESP) as a case study. Oceanography 30:100-113. https://doi.org/10.5670/oceanog.2017.427

Olins, HC, Rogers DR, Preston C, Ussler III W, Pargett D, Jensen S, Roman B, Birch JM, Scholin CA, Haroon MF and Girguis PR. 2017. Co-registered Geochemistry and Metatranscriptomics Reveal Unexpected Distributions of Microbial Activity within a Hydrothermal Vent Field. Front. Microbiol. 8:1042. https://doi.org/10.3389/fmicb.2017.01042

Baussant, T., A. Krolicka, M. Maeland, S. Ramanand, C. Boccadoro, C. Preston, R. Marin III, J. Birch, and C. Scholin in Arctic Approach, G. Sand, S. Dahle, O. A. Misund (eds). 2017. Can we use microbes to tell us about the presence of oil in water? Pp. 153-166. Fagbokforlaget.

Ryan, J., R. Kudela, J. Birch, M. Blum, H. Bowers, F. Chavez, G. Doucette, K. Hayashi, R. Marin III, C. Mikulski, J. Pennington, C. Scholin, G. smith, A. Woods, Y. Zhang. 2017. Causality of an extreme harmful algal bloom in Monterey Bay, California during the 2014-2016 northeast Pacific warm anomaly. Geophysical Research Letters. https://doi.org/10.1002/2017GL072637

Bowers, H.A., J. Ryan, R. Marin III, J. Birch, and C. Scholin. 2017. Sandwich hybridization probes for the detection of Pseudo-nitzschia species: an update to existing probes and a description of new probes. Harmful Algae 70:37-51. https://doi.org/10.1016/j.hal.2017.10.005

Bowers, H.A., Marin, R.III, Birch, J.A., Scholin, C.A., and Doucette, G.J. (2016). Recovery and identification of Pseudo-nitzschia frustlules from natural samples acquired using the Environmental Sample Processor (ESP). Journal of Phycology, 52:135–140. http://doi.org/10.1111/jpy.12369

Herfort, L., Seaton, C., Wilkin, M., Roman, B., Preston, C., Marin, R., Seitz, K., Smith, M., Haynes, V., Scholin, C., Baptista, A., Simon, H. (2016). Use of continuous, real-time observations and model simulations to achieve autonomous, adaptive sampling of microbial processes with a robotic sampler. Limnology and Oceanography: Methods, 14:50-67. http://doi.org/10.1002/lom3.10069

Yamahara, K.M., Demir-Hilton, E., Preston, C.M., Marin III, R., Pargett, D., Roman, B., Jensen, S., Birch, J.M., Boehm, A.B., Scholin, C.A. (2015). Simultaneous monitoring of fecal indicators and harmful algae using an in in situ auntomous sensor. Letters in Applied Microbiology, 61130-138. http://doi.org/10.1111/lam.12432

Aylward, F.O., Eppley, J.M., Smith, J.M., Chavez, F.P., Scholin, C.A., DeLong, E.F. (2015). Ocean basin-wide community transcriptome dynamics are conserved among microbial plankton spanning all three domains of life. Proceedings of the National Academy of Sciences (USA), 112: 5433-5448.

Varaljay, V.A., Robidart, J., Preston, C.M., Gifford, S.M., Durham, B.P., Burns, A.S., Ryan, J.P., Marin III, R., Kiene, R.P., Zehr, J.P., Scholin, C.A., Moran, M.A. (2015). Single-Taxon Field Measurements of Bacterial Gene Regulation Controlling DMSP Fate. The ISME Journal, 9: 1677–1686. http://doi.org/10.1038/ismej.2015.94

Seegers, B.N., Birch, J.M., Marin, R. III, Scholin, C.A., Caron, D.A., Seubert, E.L., Howard, M.D.A., Roberston, G.L., Jones, B.H. (2015). Subsurface seeding of surface harmful algal blooms observed through the integration of autonomous gliders, moored Environmental Sample Processors, and satellite remote sensing in Southern California. Limnology and Oceanography, 60: 754 -764.

Caron, D.A., Gellene, A., Smith, G.J., Seubert, E.L., Campbell, V., Sukhatme, G.S., Seegers, B., Jones, B.H., Lie, A.A.Y., Terrado, R., Howard, M.D.A., Kudela, R.M., Hayashi, K., Ryan, J., Birch, J., Demir-Hilton, E., Yamahara, K., Scholin, C., Mengel, M., Robertson, G. (2015). Response of phytoplankton and bacterial biomass during a wastewater effluent diversion into nearshore coastal waters. Estuarine, Coastal and Shelf Science. http://doi.org/10.1016/j.ecss.2015.09.013

Ottesen, E.A., Young, C.R., Gifford, S.M., Eppley, J.M., Marin III, R., Schuster, S.C., Scholin, C.A., DeLong, E.F. (2014). Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science, 345: 207-212. http://doi.org/10.1126/science.1252476

Robidart, J.C., Church, M.J., Ryan, J.P., Ascani, F., Wilson, S.T., Bombar, D., Marin, R. III, Richards, K.J., Karl, D.M., Scholin, C.A., Zehr, J.P. (2014). Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean. The ISME Journal 8, 1175–1185. http://doi.org/10.1038/ismej.2013.244

Ussler, W. III, Tavormina, P., Preston, C., Marin III, R., Pargett, D., Jensen, S., Roman, B., Shah, S., Girguis, P.R., Birch, J.M., Orphan, V., Scholin, C. (2013). Autonomous in situ quantitative PCR amplification of aerobic methanotroph genes in the deep sea. Environmental Science and Technology, 47: 9339−9346. http://dx.doi.org/10.1021/es4023199

Ottesen, E.A., Young, C.R., Eppley, J.M., Ryan, J.P., Chavez, F.P., Scholin, C.A., DeLong, E.F. (2013). Rhythm and synchrony of gene expression among sympatric marine microbial populations. Proceedings of the National Academy of Sciences, 110: E488-E497. http://doi.org/10.1073/pnas.1222099110

Scholin, C.A. (2013). Ecogenomic Sensors. In: Levin S.A. (ed.) Encyclopedia of Biodiversity, second edition, Volume 2, pp. 690-700. Waltham, MA: Academic Press.

Harvey, J.B.C, Ryan, J.P., Marin III, R., Preston, C.M., Alvarado, N., Scholin, C.A., Vrijenhoek, R.C. (2012). Robotic sampling, in situ monitoring and molecular detection of marine zooplankton. Journal of Experimental Marine Biology and Ecology, 413: 60–70. http://doi.org/10.1016/j.jembe.2011.11.022

Robidart, J.C, Preston, C.M., Paerl, R.W., Turk, K.A., Mosier, A.C., Francis, C.A., Scholin, C.A., Zehr, J.P. (2012). Seasonal dynamics of Synechococcus and Thaumarchaeal microbial populations in Monterey Bay resolved in real time with remote in situ instrumentation. The ISME Journal, 6: 513-523. http://doi.org/10.1038/ismej.2011.127

Saito, M.A., Bulygin, V.V., Moran, D.M., Taylor, C., Scholin, C. (2011). Examination of microbial proteome preservation techniques applicable to autonomous environmental sample collection. Frontiers in Microbiology, 2: 215. http://doi.org/10.3389/fmicb.2011.00215

Preston, C.M., Harris, A., Ryan, J.P., Roman, B., Marin III, R., Jensen, S., Everlove, C., Birch, J., Dzenitis, J.M., Pargett, D., Adachi, M., Turk, K., Zehr, J.P., Scholin, C.A. (2011). Underwater application of quantitative PCR on an ocean mooring. PLoS ONE, 6(8): e22522. http://doi.org/10.1371/journal.pone.0022522

Ottesen, E.A., Marin III, R., Preston, C.M., Young, C.R., Ryan, J.P., Scholin, C.A., DeLong, E.F. (2011). Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. The ISME Journal, 5: 1881–1895. http://doi.org/10.1038/ismej.2011.70

Ryan, J., Greenfield, D., Marin III, R., Preston, C., Roman, B., Jensen, S., Pargett, D., Birch, J., Mikulski, C., Doucette, G., Scholin, C.A. (2011). Harmful phytoplankton ecology studies using an autonomous molecular analytical and ocean observing network. Limnology and Oceanography, 56: 1255-1272.

Doucette, G.J., Mikulski, C.M., Jones K.L., King, K.L., Greenfield D.I., Marin III R., Jensen S., Roman B., Elliott C.T., Scholin, CA. (2009). Remote, subsurface detection of the algal toxin domoic acid onboard the Environmental Sample Processor: assay development and initial field trials. Harmful Algae, 8:880-888.

Scholin, C., Doucette, G., Jensen, S., Roman, B., Pargett, D., Marin III, R., Preston, C., Jones, W., Feldman, J., Everlove, C., Harris, A., Alvarado, N., Massion, E., Birch, J., Greenfield, D., Vrijenhoek, R., Mikulski, C., Jones, K. (2009). Remote detection of marine microbes, small invertebrates, harmful algae and biotoxins using the Environmental Sample Processor (ESP). Oceanography, 22: 158-167.

Preston, C., Marin III, R., Jensen, S., Feldman, J., Massion, E., DeLong, E., Suzuki, M., Wheeler, K., Cline, D., Alvarado, N., Scholin, C. (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: 1168-1180.

Greenfield, D., Marin III, R., Doucette, G.J., Mikulski, C., Jensen, S., Roman, B., Alvarado, N., Scholin, C.A. (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.

Jones, W.J., Preston, C., Marin III, R., Scholin, C., Vrijenhoek, R. (2007). A robotic molecular method for in situ detection of marine invertebrate larvae. Molecular Ecology Resources, 8: 540-550.

Roman, B., Scholin, C., Jensen, S., Massion, E., Marin III, R., Preston, C., Greenfield, D., Jones, W., Wheeler, K. (2007). Controlling a Robotic Marine Water Sampler with the Ruby Scripting Language. Journal of American Laboratory Automation, 12: 56-61.

Greenfield, D.I., Marin III, R., Jensen, S., Massion, E., Roman, B., Feldman, J., Scholin, C. (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.

Metfies, K., Töbe, K., Scholin, C., Medlin, L.K. (2006). Laboratory and field applications of ribosomal RNA probes to aid the detection and monitoring of harmful algae. In: Ecology of Harmful Algae (Granéli, E., and Turner, J.T. eds), pp. 311-325. Springer Verlag, Berlin, Heidelberg, New York.