Leadership & Staff James Birch Director of the SURF Center [javascript protected email address] Jim Birch joined MBARI in April, 2007 as the Instrument Group Leader in the Engineering department. While overseeing engineers developing instrument systems for oceanographic research, he became the project manager for the Environmental Sample Processor (ESP) project, begun by P.I. Chris Scholin in the early 2000’s. In November 2009 he moved into his current role as Director of the SURF Center (Sensors: Underwater Research of the Future). In this role he oversees all aspects of the ESP project. Jim received his B.S. from the University of North Carolina, Chapel Hill, and his M.S. and Ph.D. from the University of Michigan. He worked as a postdoctoral fellow at Northern Arizona University (Kiisa Nishikawa) and as a research scientist at the University of California, Berkeley in the lab of Michael Dickinson, where he worked on the fluid dynamics of insect flight using a scaled robotic insect model immersed in two tons of mineral oil. He continued honing his instrument design experience at Lawrence Livermore National Laboratory, working on various biodetection technologies and point-of-care diagnostic devices for biomedicine before coming to MBARI.
Zhang, Y., B. Kieft, B. W. Hobson, Q. Shemet, C. M. Preston, C. Wahl, K. J. Pitz, K. J. Benoit-Bird, J. M. Birch, F. P. Chavez, and C. A. Scholin. 2024. Coordinated and Collaborative Sampling by Two Long-Range Autonomous Underwater Vehicles. IEEE Journal of Oceanic Engineering, 49(4):1371-1382. https://doi.org/10.1109/JOE.2024.3408889
Zhang, Y., B. Kieft, B. W. Hobson, Y. Raanan, W. Ussler, C. M. Preston, R. M. Errera, P. A. Den Uyl, A. V. Woude, G. J. Doucette, S. A. Ruberg, K. D. Goodwin, J. M. Birch, and C.A. Scholin. 2024. Using a long-range autonomous underwater vehicle to find and sample harmful algal blooms in Lake Erie. Limnology and Oceanography: Methods, 22(7): 473-483. https://doi.org/10.1002/lom3.10621
Preston, C., K. Yamahara, D. Pargett, C. Weinstock, J. Birch, B. Roman, S. Jensen, B. Connon, R. Jenkins,J. Ryan, and C. Scholin. 2024. Autonomous eDNA collection using an uncrewed surface vessel over a 4200-km transect of the eastern Pacific Ocean. Environmental DNA, 6(1). https://doi.org/10.1002/edn3.468
Nowinski, B., X. Feng, C. M. Preston, J. M. Birch, H. Luo, W. B. Whitman, and M.A. Moran. 2023. Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression. The ISME Journal, 17(6): 813-822. https://doi.org/10.1038/s41396-023-01390-4
Miller, E.A., K.M. Yamahara, C. French, N. Spingarn, J.M. Birch, and K.S. Van Houtan. 2022. A Raman spectral reference library of potential anthropogenic and biological ocean polymers. Scientific Data, 9(780): 1–9. https://doi.org/10.1038/s41597-022-01883-5
Searcy, R.T., A.B. Boehm, C. Weinstock, C.M. Preston, S. Jensen, B. Roman, J.M. Birch, C.A. Scholin, K.S. Van Houtan, J.D. Kiernan, and K.M. Yamahara. 2022. High‐frequency and long‐term observations of eDNA from imperiled salmonids in a coastal stream: Temporal dynamics, relationships with environmental factors, and comparisons with conventional observations. Environmental DNA, 4(4): 776–789. https://doi.org/10.1002/edn3.293
Den Uyl, P. A., L.R. Thompson, R.M. Errera, J.M. Birch, C.M. Preston, W.I. Ussler, C.E. Yancey, S.R. Chaganti, S.A. Ruberg, G.J. Doucette, G. J. Dick, C.A. Scholin, and K.D. Goodwin. 2022. Lake Erie field trials to advance autonomous monitoring of cyanobacterial harmful algal blooms. Frontiers in Marine Science, 9: 1–18. https://doi.org/10.3389/fmars.2022.1021952
Zhang, Y., J.P. Ryan, B.W. Hobson, B. Kieft, A. Romano, B. Barone, C.M. Preston, B. Roman, B.Y. Raanan, D. Pargett, M. Dugenne, A.E. White, F. Henderikx 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: 1–11. https://doi.org/10.1126/scirobotics.abb9138
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.. 2021. An Autonomous Platform for Near Real-Time Surveillance of Harmful Algae and Their Toxins in Dynamic Coastal Shelf Environments. Journal of Marine Science and Engineering, 9(3): 336. https://doi.org/10.3390/jmse9030336
Sepulveda, A. J., A. Hoegh, J. A. Gage, S. L. Caldwell Eldridge, J. M. Birch, C. Stratton, P. R. Hutchins, and E. P. Barnhart. 2021. Integrating Environmental DNA Results With Diverse Data Sets to Improve Biosurveillance of River Health. Frontiers in Ecology and Evolution, 9(620715). https://doi.org/10.3389/fevo.2021.620715
Zhang, Y., B. Kieft, B.W. Hobson, B.Y. Raanan, S. Urmy, K.J. Pitz, C.M. Preston, B. Roman, K.J. Benoit-Bird, J.M. Birch, F.P. Chavez, and C.A. Scholin. 2021. Persistent sampling of vertically migrating biological layers by an autonomous underwater vehicle within the beam of a seabed-mounted echosounder. IEEE Journal of Oceanic Engineering, 46: 497–508. https://doi.org/10.1109/JOE.2020.2982811
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
Sepulveda, A.J., J.M. Birch, E.P. Barnhart, C.M. Merkes, K.M. Yamahara, R. Marin III, S.M. Kinsey, P.R. Wright, and C. Schmid. 2020. Robotic environmental DNA bio-surveillance of freshwater health. Scientific Reports, 10: 1–8. https://doi.org/10.1038/s41598-020-71304-3
Evans, S., J. Birch, J. Breier Jr., M. Jakuba, M. Saito, and J. Robidart. 2019. Ocean robots uncover microbial secrets. Microbiology Today, Oceans(February 2019): 18–21. https://microbiologysociety.org/publication/past-issues/oceans.html
Nowinski, B., C.B. Smith, C.M. Thomas, K. Esson, R. Marin III, C.M. Preston, J.M. Birch, C.A. Scholin, M. Huntemann, A. Clum, B. Foster, B. Foster, S. Roux, K. Palaniappan, N. Varghese, S. Mukherjee, T.K.B. Reddy, C. Daum, A. Copeland, I.M.A. Chen, N.N. Ivanova, N.C. Kyrpides, T. Glavina del Rio, W.B. Whitman, R.P. Kiene, E.A. Eloe-Fadrosh, and M.A. Moran. 2019. Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom. Scientific Data, 6: 1–7. https://doi.org/10.1038/s41597-019-0132-4
Yamahara, K.M., C.M. Preston, J. Birch, K.R. Walz, R. Marin III, S. Jensen, D. Pargett, B. Roman, W. Ussler III, Y. Zhang, J. Ryan, B. Hobson, B. Kieft, B.Y. Raanan, K.D. Goodwin, F.P. Chavez, and C.A. Scholin. 2019. In situ Autonomous Acquisition and Preservation of Marine Environmental DNA Using an Autonomous Underwater Vehicle. Frontiers in Marine Science, 6: 1–14. https://doi.org/10.3389/fmars.2019.00373
Zhang, Y., J.P. Ryan, B. Kieft, B.W. Hobson, R.S. McEwen, M.A. Godin, J.B. Harvey, B. Barone, J.G. Bellingham, J.M. Birch, C.A. Scholin, and F.P. Chavez. 2019. Targeted sampling by autonomous underwater vehicles. Frontiers in Marine Science, 6: 1–12. https://doi.org/10.3389/fmars.2019.00415
Nowinski, B., J. Motard-Cote, M. Landa, C.M. Preston, C.A. Scholin, J.M. Birch, R.P. Kiene, and M.A. Moran. 2019. Microdiversity and temporal dynamics of marine bacterial dimethylsulfoniopropionate genes. Environmental Microbiology, 21: 1687–1701. https://doi.org/10.1111/1462-2920.14560
Kiene, R.P., B. Nowinski, K. Esson, C. Preston, R. Marin III, J. Birch, C. Scholin, J. Ryan, and M.A. Moran. 2019. Unprecedented DMSP Concentrations in a Massive Dinoflagellate Bloom in Monterey Bay, CA. Geophysical Research Letters, 46: 12279–12288. https://doi.org/10.1029/2019GL085496
Krolicka, A., C. Boccadoro, M.M. Nilsen, E. Demir-Hilton, J. Birch, C. Preston, C. Scholin, and T. Baussant. 2019. Identification of microbial key-indicators of oil contamination at sea through tracking of oil biotransformation: An Arctic field and laboratory study. Science of the Total Environment, 696: 1–13. https://doi.org/10.1016/j.scitotenv.2019.133715
Birch, J.M. 2018. Collecting and processing samples in remote and dangerous places: The environmental sample processor as a case study. Pure and Applied Chemistry, 90: 1625–1630. https://doi.org/10.1515/pac-2018-0201
Bowers, H.A., J.P. Ryan, K. Hayashi, A.L. Woods, R. Marin III, G.J. Smith, K.A. Hubbard, G. Doucette, C. Mikulski, A.G. Gellene, Y. Zhang, R. Kudela, D. Caron, J. Birch, and C. Scholin. 2018. Diversity and toxicity of Pseudo-nitzschia species in Monterey Bay: Perspectives from targeted and adaptive sampling. Harmful Algae, 78: 129–141. https://doi.org/10.1016/j.hal.2018.08.006
Birch, J.M., B. Barone, E. DeLong, G. Foreman, K. Gomes, B. Hobson, S. Jensen, D.M. Karl, B. Kieft, T. O'Reilly, D. Pargett, C. Preston, B. Roman, A. Romano, J. Ryan, C.A. Scholin, W. Ussler, K. Yamahara, and Y. Zhang. 2018. Autonomous targeted sampling of the deep chlorophyll maximum layer in a subtropical north Pacific eddy. OCEANS 2018 MTS/IEEE Charleston, pp. 1-5. doi: 10.1109/OCEANS.2018.8604898.
Hobson, B., B. Kieft, B.Y. Raanan, Y. Zhang, J. Birch, J.P. Ryan, and F.P. Chavez. 2018. An autonomous vehicle-based open ocean Lagrangian observatory. 2018 IEEE OES Autonomous Underwater Vehicle Symposium, Porto, 6–9 November 2018. IEEE Oceanic Engineering Society, Laboratório de Sistemas e Tecnologia Subaquática, Universidade do Porto.
Scholin, C.A., J. Birch, S. Jensen, R. Marin III, E. Massion, D. Pargett, C. Preston, B. Roman, and W. Ussler III. 2017. 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, H.C., D.R. Rogers, C. Preston, W. Ussler III, D. Pargett, S. Jensen, B. Roman, J.M. Birch, C.A. Scholin, M.F. Haroon, and P.R. Girguis. 2017. Co-registered Geochemistry and Metatranscriptomics Reveal Unexpected Distributions of Microbial Activity within a Hydrothermal Vent Field. Frontiers in Microbiology, 8: 1–18. https://doi.org/10.3389/fmicb.2017.01042
Ryan, J.P., R.M. Kudela, J.M. Birch, M. Blum, H.A. Bowers, F.P. Chavez, G.J. Doucette, K. Hayashi, R. Marin III, C.M. Mikulski, T. Pennington, C.A. Scholin, G.J. Smith, A. Woods, and 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, 44: 5571–5579. https://doi.org/10.1002/2017GL072637
Caron, D.A., A.G. Gellene, J. Smith, E.L. Seubert, V. Campbell, G.S. Sukhatme, B. Seegers, B.H. Jones, A.A.Y. Lie, R. Terrado, M.D.A. Howard, R.M. Kudela, K. Hayashi, J. Ryan, J. Birch, E. Demir-Hilton, K. Yamahara, C. Scholin, M. Mengel, and G. Robertson. 2017. Response of phytoplankton and bacterial biomass during a wastewater effluent diversion into nearshore coastal waters. Estuarine, Coastal and Shelf Science, 186: 223–236. http://dx.doi.org/10.1016/j.ecss.2015.09.013
Bowers, H.A., J. Ryan, R. Marin III, J.M. Birch, and C.A. Scholin. 2017. Sandwich hybridization probes for the detection of Pseudo-nitzschia (Bacillariophyceae) 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., R. Marin III, J.M. Birch, C.A. Scholin, and G.J. Doucette. 2016. Recovery and identification of Pseudo-nitzschia (Bacillariophyceae) frustules from natural samples acquired using the environmental sample processor. Journal of Phycology, 52: 135–140. http://dx.doi.org/10.1111/jpy.12369
Zhang, Y., B. Kieft, R. McEwen, M.J. Stanway, J. Bellingham, J. Ryan, B. Hobson, D. Pargett, J. Birch, and C. Scholin. 2015. Tracking and sampling of a phytoplankton patch by an autonomous underwater vehicle in drifting mode. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Oceans Conference, Genova, 18–21 May 2015.
Seegers, B.N., J.M. Birch, R. Marin, C.A. Scholin, D.A. Caron, E.L. Seubert, M.D.A. Howard, G.L. Robertson, and B.H. Jones. 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. http://dx.doi.org/10.1002/lno.10082
Yamahara, K.M., E. Demir-Hilton, C.M. Preston, R. Marin III, D. Pargett, B. Roman, S. Jensen, J.M. Birch, A.B. Boehm, and C.A. Scholin. 2015. Simultaneous monitoring of faecal indicators and harmful algae using an in-situ autonomous sensor. Letters in Applied Microbiology, 61: 130–138. http://dx.doi.org/10.1111/lam.12432
Pargett, D.M., J.M. Birch, C.M. Preston, J.P. Ryan, Y. Zhang, and C.A. Scholin. 2015. Development of a mobile ecogenomic sensor. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers Oceans Conference, 2015: 1–6.
Pargett, D.M., S.D. Jensen, B.A. Roman, C.M. Preston, W. Ussler III, P.R. Girguis, R. Marin III, J.M. Birch, and C.A. Scholin. 2013. Deep water instrument for microbial identification, quantification, and archiving. Proceedings of Marine Technology Society/Institute of Electrical and Electronics Engineers Oceans '13, San Diego, 23–26 September 2013.
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. http://dx.doi.org/10.1021/es4023199
Ryan, J., D. Greenfield, R. Marin III, C. Preston, B. Roman, S. Jensen, D. Pargett, J. Birch, C. Mikulski, G. Doucette, and C. Scholin. 2011. Harmful phytoplankton ecology studies using an autonomous molecular analytical and ocean observing network. Limnology and Oceanography, 56: 1255–1272. http://dx.doi.org/10.4319/lo.2011.56.4.1255
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. http://dx.doi.org/10.1371/journal.pone.0022522
Preston, C.M., R. Marin III, S.D. Jensen, J. Feldman, J.M. Birch, E.I. Massion, E.F. DeLong, M. Suzuki, K. Wheeler, and C.A. 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: 1168–1180.
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.C. 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: 158–167.